I would think if your going to do it this way (splitting equipment between two diff breakers) it would only matter to have the powerheads split. I only mention it because lets say you have your return pump on breaker A and your skimmer on breaker B. If A trips then it doesn't really matter if your skimmer is still going, not to mention it will just bubble over back into the sump. Same goes for the heater. If the return pump gets shut off some how it doesn't matter that any of the equipment down in the sump are still working because the sump is effectively cut off from the display. So lets say you have your return pump on a really good battery back up so it DOESNT shut off when the breaker trips..... Then it's a great idea to split the equipment up so that you still have some kind of life support still on the tank.
It's early and I'm still tired. I may be way off base here. If I am.... Sorry