I thought I would drop in my 2 credits. As a GM, it's boring to stop the action every time there's some minor (under 100 cred) payment that needs to be made. I note that stuff down ("leaving Formos, customs fees on c600 cargo", etc.) and then when I distribute xp and creds later, the minor payments come out first. That way ship maintenance, docking fees, customs, licenses, etc. are all handled after the session and not in the middle. This works for both SW games that I've GMed (different systems) where the party is/is becoming a mutually-dependent group and is not one with a history of working together.
If the payments come up in game for whatever reason, the players can RP that stuff out in game. "What do you mean you need creds for a drink?" "I used my last 15 yesterday to pay your stupid docking fee. It was my turn, remember?" Whether the captain is charging the crew for each hop, giving them a total bill at the end, they take turns paying, whatever; it's not necessary for us to track all those details in game unless it comes up. This also gives the players more freedom to RP without trying to remember who has paid for what. I use a similar system for misc. credits - if you are searching an Imperial official's office for loot, you may find "assorted small tech items worth around 50 credits" and I note that, and once your character has a chance to visit a merchant/marketplace/fence I will award you the credits. There's no need to track this 5 credit datapad, and a 12 credit hyperspanner, etc.
As far as ship upgrades and crew payments go - I definitely leave that up to each group at any given point. I have several suggestions on this thread, and they all work for different groups. Personally, I prefer an approach that puts the focus on the characters and narratives and not so much on their pocketbooks and character sheets. :-)