hey T_Ross, I am no expert with this as well, but I have tinkered with my acoustic guitars quite a bit. I have found that slight adjustments to the truss rod usually solve the problem, and generally will not affect the intonation. I like my action/relief pretty low, and I find that when the seasons change (pennsylvania), that I usually need to make a minor adjustment. Intonation never went out of whack for me.
Good luck!
Leonidas' Gear List:
Electric Guitars - Agile AL-2800 (S.D. '59 B, Pearly Gates N), Squier Telecaster Custom (GFS FAT PAFs + Mods)
Acoustic Guitars - Crafter ML-Rose, Epiphone PR-350CE
Amps - VOX AD50VT, Epiphone Valve Jr. (Modded), Fender Blues Jr
Pedals - Crybaby Classic w/ Fasel Inductor, Boss DS-1, Digitech Bad Monkey, Danelectro Cool Cat Chorus, Danelectro Fish & Chips EQ, Ibanez AW7