Yes, eventually you want water to get on top. This is where all the gas exchange occurs.
Without PHs, the water on the sides/corners will be stale. You'll have too much detrius/co2 build-up at those places.
Dont be afraid to go high on the powerheads. I don't believe the emporer 400 can pump 400 gph. The pump may be rated at 400 but when hung 3 inches above water, go through 2 90's elbows, the actual flow through the emporer will be halved.