I have my heater on its side towereds the bottom in the back. I have a hydor 3 about 2 inches above it running the length of the heater. Wont this make the heater stay on all the time? Should I move the Hydor back up to the top away from the heater?
You are fine.
Having a PH on the heater may actually make the heater run less, since the PH is generating heat, which it is transferring to the water flowing through it, but this is minor when compared to the output of the heater.