Hey Dan, the chambers' unevenness is totally normal. It's nearly impossible to have each baffle be perfectly symmetrical on both sides, so one side will always run a little lower than the other. You also want to make sure the chamber where the pump is located is running lower than the other chamber to ensure there are no stagnant spots in your rear chambers. You want to put your ATO sensor on the side that runs the lowest. For me, this is the right chamber (when looking directly at the front glass panel). I have my water level roughly 3 inches or so above the pump. Then my ATO input line is on the left chamber above the pump. I haven't had any issues with this setup so far. I'll replace the pumps with some DC pumps once they start to cause problems but so far they've been perfectly fine.