Mike,
If your pond is 1/10th of an acre and you have that kind of diversity, your issues are more than when to aerate.
That said, your issues concerning temps are valid in the summer. I doubt that running your aerator in the winter will cause you any issues. Further, I don't know that you will be able to warm your water much in the winter months, but running during the daylight hours will not hurt your temps as much as it would at night.
What is your goal for aerating? If it is only water temp control, then your schedule should help. If you are trying to promote good bacteria to control muck buildup, I would run the system 24/7when possible.
In short, give us the problem you are trying to fix and the experts (not me)should be able to help you.
