I am not familiar with how your system works, but typically people put ATOs in the sump portion of their tank because the overflow system means the display tank water level will always be the same (if it gets any higher, it drains) while the sump water level can fall if there is evaporation or water is otherwise removed from the system.
I am guessing you have an all-in-one system, and the rear of your tank acts as the sump? The same basic principle should apply here. As long as the pump is working water should reach a set level in the display portion of the tank, then pour back into the rear chambers. This should continue until the rear chambers get to be so low the pump can no longer work.
For the water level to be falling in the display portion of the tank, but not the rear, it would seem to imply they weren't plumbed together properly at all. Are you using a under-tank sump as well? If so, that's where the ATO should be pumping, not the rear chamber.