Strange. Sounds like whom ever installed the ballast system had a great ear. They must have known right when to turn the pumps off. I have never seen a Supreme with reversible pumps from the factory. They are the only manufacturer that I know of that still transom mounts the Attwood Tsunami 1200
Jamie, You are correct. By adding a tee fitting and two check valves per pump you can divert the water to drain above the water line. I have attached a diagram below.
You will need to decide if you are going to add a new thru-hull for the drain or if you are going to try and use the vent port that is already in use. If you are going to share the port you will need another wye or tee and another check valve. This will prevent water from pushing back into the vent port when draining.