I've been riding a fixie on the trainer for about 10 years now. However, I only ride it on recovery days(or after weightligting) with very little resisitance.

Fixed gear in hilly terrain is not that bad if you are discreet about your gear choices, alot of fun even, but as for the trainer, why not? If you can alter the resistance by some other way besides shifting gears, just like most trainers these days, then it shouldn't be any trouble at all.

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"Maybe you should just run faster..." TM

The real challenge is riding your fixie on your rollers. The main issue with the fixie indoors is finding an appropriate gearing for your workout.

right now the gearing is setup as 42x15 I think? I have 48 & 50t chainrings and I have a 17t cog too. The levels of resistance on my trainer are pretty lame. so, considering that the current setup of 42x15 works for me pretty well, should I switch to the 48 for the trainer? Maybe I should just leave it to trial and error and ditch it if it becomes a total pain in the ass.
as far as usage of the bike on the hills, i am more concerned about having enough legs to make it down the other side once i get up.

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Partially-Hydrogenated