Or accept that Rokugan isn't a capitalistic economical system. It is a feudal agrarian barter economy.
Unlike the money as we know and use today, a koku doesn't have any intrinsic value on its own. Instead it is a symbol (technically, an IOU but we'll get back to that.) for something that has value in Rokugan. Rice! That means you can't earn koku, you can only grow it.
(This is incidental the reason why money and commerce is seen as something dirty and unbecoming for a samurai. Rice is produced, grown, through manual labour and a honourable samurai should stand above manual labour. As a koku is a symbol for rice, it by association is also symbol for manual labour. So just as an honourable samurai should stand above manual labour he/she must also stand above money and commerce.)
So how does it affect the economy in Rokugan. In other words, how does it all work.
To start with no rice, no koku. This is a literal truth. Each koku represent the amount of rice it takes to feed a peasant with rice for one whole year. (In the real world in edo period Japan that was about 5 bushels. Don't ask me how much that is.) Each great clan mint their own coinage each year based on their harvest. Minus what they owe in taxes to the emperor. Why minus what they owe in taxes? Because the tax to the emperor is literally paid in rice. So each clan have to lug thousands sacks of rice to the emperor to pay their taxes. (And I assume that based on the rice he receive the emperor in turn mint his own koku.)
So let say, the great and awesome Pokemon clan grows a 1000 bushels of rice a good year. Now the emperor will want his share which will most likely be a lions share, let's for the sake of convenience say half but it would probably be more. This leaves the Pokemon clan with 500 bushels of rice to mint koku from. Except they need to eat some of the rice to survive so in the end they only have 200 bushels left. 200/5 = 40. So in the end the Pokemon clan is the not so rich owners of 40 koku to trade with.
Unfortunately, next year there is a drought and the Pokemon clan only managed to grown 800 bushels of rice. Oy vey. Of course the emperor still require his cut of half their harvest leaving them with only 400 bushels and they still need to eat. Can't let the peasants starve to death as they are needed to grow the next year's harvest. No peasants, no harvest and the clan is bankrupt. So the bad year the Pokemon clan is only able to mint 20 koku. The bad harvest literally cut the clans fortune in half.
Of course, not all clans is as lucky as the Pokemon clan by being able to grow their own rice. The Dragon clan's lands are located in the mountains of Great Wall of the North, which isn't exactly good rice growing country. Yet the tax to the emperor still have to be paid in rice. Luckily, the dragon clan have rich mines. So they instead of grow rice, they mine iron and then goes to their good friends the Lion clan who has fertile rice growing lands and says; "Hey buddies, you want to go to war and need swords for that. You grow more rice than you need on your lands but you can't grow swords. Luckily, I have all the ore for swords you need and I will give the ore for all the rice you can spare." And so the two clans barter ore for rice so that the Lion can go to war with new swords and the dragon can pay their taxes.
And most commerce and trade in Rokugan has that character. A straight up barter of goods. From the peasant trading a chicken for a new knife to a great clan trading a valuable commodity for another, with rice being the most valuable.
The need for koku is rare and is generally only used when a person or clan doesn't have a commodity the other part wants.
Let's say the proud Lion doesn't want new swords as everyone knows that the old swords the ancestors used is so much better so they don't want to trade with the Dragon clan for ore. Luckily, the Phoenix clan wants the Dragon's ore for bells in their temples and shrines. Now the Phoenix clan can grow their own rice but only enough for their own needs, in other words enough to pay their taxes. However, as fate would have it the Phoenix clan just traded a bunch of wood to the Crane clan to be made into three-ply toilet paper as the Crane clan is far too sensitive to use mere two-ply paper. But as mentioned the Phoenix clan grows all the rice it needs so the Crane clan gave them a large pile of koku instead of rice.
Now, the Phoenix clan can't give the Dragon the rice it needs but it can give the Dragon clan the koku it got from the Crane. So they trade ore for koku.
Of course, the Dragon still needs rice so it has to go to the Crane clan and say; "look I got a pile of your koku. I want the rice this represent." And the Crane clan has no other choice but to hand it over or admit that they are cheats and frauds and that their coin doesn't have any value. So naturally, the Crane take back their koku and happily give the Dragon rice instead.
Which shows how koku is nothing more than a symbol for rice and how it's value stems from it being a substitute, an IOU, for a fixed amount of rice. Unlike a gold coin in DnD whose value comes from the amount a gold it contain or a dollar whose value comes from what certain economical institutions agree on what it value is.
Which in turn is a segue to commerce in Rokugan. A clan needs more than just rice to function. It needs steel for tools, weapons and armour. Jade and other precious stones for protection and jewellery. Wood for construction and paper. And so on. Most of which they need to turn to another clan to get or rather trade. Most of the time it will probably be a straight up trade or barter. Other times koku is substituted as payment. But the purpose of every trade, every deal is to provide for the needs of the clan.
Unlike, in a capitalistic society like our own, the goal of commerce in Rokugan isn't to make a profit but to ensure that the clan has everything it needs to function. Once it that is accomplish there is little need for any further trade. The reason the Crane clan is one of the most powerful clans in Rokugan (at least before recent events in the lore) is because it is largely self-sustaining while producing a large surplus in rice. Instead, of lining their coffers by selling the surplus for a profit as we would expect in our society, they give the surplus away as gifts to less fortunate clans in return for future favours in court. Essentially the Crane pay the other clans' taxes to get their support in the emperors court.
The focus of commerce on providing for the clan's needs instead of profit is the reason there are no real merchant guilds or independent merchants in Rokugan. At least not above the level of shop owners or itinerant peddlers. If you trade in bulk you most certainly does it in the service of a clan. Of course, since money equal labour which a honourable samurai should be above, the clans need Bonge middlemen to act as merchants though under the strict guidance of a Samurai patron. But even they should take care not to do it for a profit.
Naturally, every one wants to make a good deal and it's only human to want something extra for your trouble (especially as a bonge merchant) but to be in it to make as huge profit as possible is more than frowned on. For a Samurai it can even be against Bushido. It is the reason way materialism is something negative for a character. For the same reason a very dutiful and honourable samurai patron might not take or receive anything extra from the commerce he/she controls, being perfectly happy with what his/her lord provides.
Now why might that be. It brings us to the feudal part of Rokugan economy and player characters personally economy. The most valuable commodity is as we have establish rice. The reason for this is because rice comes from the land and all land in Rokugan belongs to the emperor making it sacred. Thus all rice in Rokugan belong to the emperor and everyone else, from the lowest hinnin to the loftiest Clan Champion, is there to serve the emperor by taking care of the land. In return the emperor graciously grant every person in Rokugan a suitable stipend for their station in return for their service to him and the land.
A peasant grows the emperor's rice and in return is allowed to keep enough food for his family to live on until the next harvest. A local lord collects the rice and administer the villages under is charge and in return is allowed to live in large house with servants to care for his needs and ji-samurai to help him protect the land. The local lord gives the rice to a provincial daimyon, who in turn maintain the province infrastructure and keeps an army for its defence. For this the Daimyon receives a castle with hundreds of servants and samurai to assist him in his duties. The daimyon gives the rice to the clan champion who gets a even bigger castle and in return gives the rice to the emperor. Who, assumedly, spends most of his time eating a **** load of rice.
Now practically this stipend comes from your clan and is granted by the guy above you in the hierarchy but technically it comes from the emperor.
Which brings us back to the problem with making a profit. By making a profit you are taking more than your share of rice and the guy you're taking it from is none other the the sacred Emperor himself. Making a profit in Rokugan is literally stealing from god.
Which finally brings us to the OP's question "How do you Koku?".
The short answer is: You don't. You just don't steal from god.
The longer answer is: You don't because it is assumed that your lord has provided you with everything you need to perform your duties according to your station. This includes full room and board, medical services, clothing and any other accoutrements you might need. If something breaks, you go to your lord for him to replace it or pay for its repairs. If you duties change so you need new equipment you go to your lord for him to grant it. If you lack something you need to perform your duties, you go to your lord for him to provide it. And if he doesn't you can protest to your lord, hoping he will change his mind. If he doesn't you can either accept it and make do, keep protesting by either leaving his service by joining the Brotherhood or committing seppuku. Unless, you think his refusal is gross negligence in which case you can go to your lord's lord and complain. In which case there are really only two outcomes. Either your lord's lord agrees with you by making your lord commit seppuku for his negligence with you doing the same next to him for ratting out your boss. Or he disagrees with you and you still have to kill yourself for telling on your boss.
Of course, the stipend often include coin in the form of a few koku. Someone mention treating the starting koku as an allowance. I'd say that is spot on. Normally I'd say that represented the amount of a yearly allowance because that was basically what it was. But because of the actually prices in the rulebook if I ran a game I'd probably treat them as a monthly allowance. (1 bu for a bottle of sake is the real world equivalent of a 1000 dollar bottle of champagne).
(Don't forget that the 4-5 koku you get is really a crap load of money. 1 koku represent the amount a peasant need to live on for a year. It is a year's wage for a peasant so as a samurai that coin is equivalent of a 6 figure salary in the real world.)
Now you're not supposed to use the money to buy equipment or stuff you need for yourself. That would be insulting to your lord. Basically, stating for anyone to see that he is unable to care for his subject and claiming he is unable to perform his duty.
So what do you use the koku for if not for stuff for yourself. Mostly, you use it for gifts and entertainment. Gift giving is important so most of the stuff you buy should be for others including your lord. Of course, going to a tea house or the theatre isn't free but everyone even samurai needs to relax and enjoy themselves at times. (And bullying innkeepers to get free drinks usually only works once or twice.)
The koku is also there so you can support yourself when your lord can't do it directly. For example when you travel through another clan's lands. Your lord has no power to provide for you there but through the allowance he can still do so indirectly thus fulfilling his obligation to you as his lord.
From a gaming perspective, forget about players earning gold DnD style, forget about them going shopping for gear. Just give them when you think they need and if they want anything else make them make their case in front of their lord and decide if it is good enough for him to relent, through dice rolls or roleplay is up to you. And if they want something they shouldn't have just deny them.
They want a rope for a mission, just make them go to the castles store room and take one.
They're going to war, have their lord give the armour they need, and once the war is over have the lord take it back.
The courtier wants a cool katan like the one the bushi have. Tell him to forget it. It's not part of his duty and should never be.
And only make them pay cash for something when they are in a situation where their lord can't or shouldn't do it for them.