What I do is pick the thing I really want to try out, then just make guesses for a trial run. If I think I'll run out of ammo I'll equip that, for example. Then during the run, take notes of what's not going to work, like if bugs are surviving but one damage upgrade can kill them, or the reload is taking too long, etc.
TL,DR: just pick something that looks cool and fix it over time.