You aren't alone in that issue, I have the same one. 3/4 or 6/8 can cause issues. Especially if you are playing triplets and end up with an odd number of notes in a measure. In that case the time signature could alternately be written as 9/8. I ran into that on Jesu, Joy of Man's Desiring. The good thing about that particular song is that there are almost no rests or quarter notes. As a result it was odd only if you were watching the music and observing that you were playing an up stroke at the start of every other measure. In cases like that, I just alternate all the way through. When you do add rests or longer notes is when you have to make some decisions. I don't think there is a hard and fast rule in that case. I would suggest just figuring out what is most natural for you as far as landing you on significant down beats (such as 1) with a down stroke, or perhaps even what makes sense for where you want accents. When mixing triplets and straight eighths, I try to end the triplet phrase back on "normal" up down picking, but that's just me. At some point, a phrase can get so difficult to make it work out "right" that I just commit the tune to memory and see how I naturally am inclined to play it, then I make note of it and try to repeat it from that point forward.
Best of luck and if you figure out some things that help, please pass them along.