Each class has a different way to give feats. But when you get a prestige class, what feats distribution prevails : the one of the first class or of the prestige class ? or a mix of the two ?

prestige.

Yeah, the prestige class.

 

You gain feats according to the level in the class you are leveling up. Since in the KOTOR series, you stop gaining levels in your old class once you get your new class, it's really cut and dry; you don't even need to think about what class you're leveling this time.