It is quite possible to only play with two people, indeed you have more time to devote to each pc if you have fewer people to deal with. One can even do solo adventures if they only have one player available, want to do a background game, the party splits up, etc.
If you are only planning on running a few sessions I would strongly recommend playing one of the prefabricated adventures which have been made available; this way you can work more on polishing your style than coming up with a scenario.
Things to consider:
Don't give out too much loot. I know that, as a player, you start getting the idea that you'd love to have tons of 'sweet loot', so as GM you start giving it out like candy ... the problem is, you end up making characters too powerful and destroying game balance. Soon, all the loot makes the game less fun, rather than more.
Do give out some items, however. In rpgs acquiring items is sometimes considered your reward for overcoming difficult obstacles, so failing to give out anything is almost as bad as giving out too much. Mind you, if you were playing more than a few sessions, I would recommend some of that reward come in the form of npc contacts, allies, further plot hooks related to character backgrounds, and so forth. Not every reward need be a double barreled, fully automatic, melta cannon.
Don't take the spotlight away from the characters. This is their adventure and while it is true there is a vast galaxy out there, with its own very involved politics and countless powerful people/organizations with their own agendas, the pcs should still feel as though they are at the center of their adventure. (not the center of the universe, by any means, but they should feel they are stars - don't make their npcs outshine them on a regular basis - though they should be in awe and/or fear of their inquisitor) This can occasionally be a difficult one to achieve ... I know that I love to flesh out the entire setting and set the players down in it to run about and experience what they will, but sometimes the pcs get lost in the midst of everything else which is going on in the background - be careful of that.
Read the GM advice in the setting handbook. This can be very useful for a new GM, as it lays out some of the very basic rules of taking on that mantle.
Be prepared - know where the proper crit charts, monster stats, weapon stats, etc. are and mark them with post it notes or something similar so you can flip quickly to the information. Nothing disrupts a game like having to flip through a book in the middle of an encounter.
Don't let pcs push you around. You are the GM, if you make a ruling it is done, move on. If a player brings up a very valid point, such as you forgetting a rule or something being inconsistant, then you can give it some quick thought and possibly rectify the mistake, but do not get into protracted arguments with players over rule interpretation, damage sustained, etc. If a player has a significant issue, tell him you can talk about it after the session is over.
Be fair and don't let the power go to your head. While you are the GM, part of what that means is adjudicating things fairly, not playing favorites and letting players get ahead once in awhile. Remember, you have the power to kill players any time you like, hence this is not a battle between you and them - you are playing the game TOGETHER.
Everyone should be enjoying themselves, this includes you. If people aren't having fun, take a moment to reflect and figure out what is going wrong, then make an effort to fix it. If people aren't enjoying the game, then it becomes a chore and no one likes chores.
Have a solid idea for your adventure, make certain you know who the major npcs are, what the major events are, where the pcs are going, what the goal is, etc. The better you know what you want, the smoother the game unravel.
Be willing to bend. While having a solid idea is important, be willing to bend it when necessary ... players will do things you never anticipated and, rather than force them back to a linear plotline, try adapting the scenario to the things they do. They decide they don't want to talk to the local magistrate, but instead hang out in the bar - have npcs drop rumors about the adventure. They decide they are going to rob the town rather than save it - have the monster attack hit when they are about half done, so they are forced to react in some way. (though if they've decided to rob the town, chances are they'll be looking for a way to escape, not play the heroes ... but this can be fun too)
Be descriptive ... what are the players seeing? Hearing? Smelling? Always include more than one sensation when you describe something: "The dockhand unloading your stuff looks like he was an ork switched with a human at birth. Under a layer of fat his muslces bulge like ripe melons and his face twists into groteque shapes with the effort of moving crates. The smell of sweat, like rotting meat, hangs around him like a nimbus, attracting flies whose hypnotic drone cause you to forget where you are for a long moment. When he passes close the smell sticks to the roof of your mouth and you realize you'd better give him room if you don't want to spoil your dinner - or revisit your lunch."
Less can be more. While description is important, be certain to leave something to the players' imaginations. If you overdescribe every scene you not only slow down the game, but pcs feel suffocated. Describe enough to set the stage, add some atmospheric details, then let the scene play out. If something is unclear, the players will ask you to fill in the blank, so don't be too affraid of them missing some small detail. (though, if they are missing something you'd like them to notice, use an npc to draw attention to it ... have the npc mention it, bump into it, look at it curiously, etc.
Don't let the dice tell your story. Though dice are a useful tool, they cannot do your job for you. Only call for rolls when the outcome is important, otherwise let people do things appropriate to their character and stats without calling for a skill check. If the pc has a high strength, let him move those stones, if he has a high intelligence let him figure out minor details, etc. If you use the dice too often, they become routine and boring - if used only when neccessary, the players will quickly come to recognize when something is important. (though, sometimes it can be fun to require a roll when it isn't a big deal, just to keep players guessing)
And so much more ... I think I'll stop here and give someone else an opportunity to comment.