I would have thought you would generally leave the time signature as simple as possible to make counting easier and then screw the drummer over .
I played Messiaen's Turangalila symphony the other week and throughout there were sections where the time signature was constant, say, 4/8 and every 2 or 3 bars the same thing would come back but offset by a semiquaver. I can't remember if this was because the instruments with a more significant part were playing in 4/8 or if he just thought 17/16 would be ridiculous, I was too busy counting...
Anyway, I would put the harder part to play/read in its time signature and make everything else follow that. I have been in a couple of prog metal bands and a death indie band also with lots of polyrhythms, although I played the guitar I usually thought of it as being in the time signature of whatever the drummer was playing in but that could have been because he usually had the more complicated part...