My 2003 has a similar setup. One of the port side thru hulls is the vent for the port side rear tank and the other is one of the common drains. On the starboard side in the rear, there is the vent for the starboard side rear tank, the common drain, and the rear bilge thru hull. On the starboard side further forward should be the vent for the kgb and the forward bilge thru hull.
The distribution manufold should have 5 lines going into it. The largest is from the water pickup on the bottom of the boat. The next 3 largest should run to each pump, and the other two are for the common drains. I think there is a check valve on the large pickup line that prevents the water from draining out the bottom when the pumps and in reverse and forces the water to the drains above the waterline in the back.