Well crap. Sorry Lauren :(
I think temping is a good idea. It will give you a better idea of what is going on with your cycles. I temp orally and I don't always temp through AF but its only because I have a pretty good idea of what my cycles look like at this point. I have definitely read that temping vaginally gives more accurate results.
Normally you want to take it after at least a few hours of solid sleep. If you get up to pee in the night, I would still just temp at your normal wake up time. Try to take it at the same time every day but don't stress if you can't, it should still be pretty close. DS still wakes up in the night so my sleep is not consistent at all but I can still tell when I O based on my temps.