To fill the tank you open a flap valve at the top of the tank using a servo. As the tank is already vented at the bottom, the air escapes, and the chamber floods.
To blow ballast, the air pump sucks in air from the surface (via a snorkel pipe). With the flap valve closed, the water is pushed out back through the vents on the bottom of the cylinder, whence it came. The pumps are diaphragm based, so aren't adversely affected by ingesting a bit of water, you shouldn't use a piston based pump for this system.
Do bear in mind that you need to ballast your boat so that it is just positively buoyant, or you will need to drive your boat to the surface to clear your tank. If you have a gas system fitted too, then that isn't necessary (belt and braces).