In general finishing an episode (adventure) gives you 1 XP you can spend to add a +1 bonus to a skill you have, or add a new skill to your character. This is great for short term play, but in long term play-it blows up.
If you plan on a campaign I'd recommend the following:
Improving a skill: The cost equals the new level +1 XP. So if you are going from level 2 to level 3 in a skill, it would be 4XP (3 for the new level +1) Learning a new skill costs 2xp points.
Double the ability price for a new one to 8xp and use the same "new level +1 price" when pricing to increase abilities.
The reason for no levels in the game is because the game assumes players are all important crew members on board already like Spock, McCoy, Kirk, Scotty, etc.
So what to do in a long term game to reward and motivate players? One word: Ships.
In my own game, I used ships as a "level" device. As the players increased in "level", they got promoted to a new (to them) and bigger ship. So start them on a small scientific research ship and let them earn their way into bigger ships! That's the best and most "tangible" reward for players in the Far Trek Universe. A good referee makes sure its a blessing...and a curse! :)