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The drain features you describe were from the factory, and on all Whaler Drive/Full Transom 22's and 25's.

The transom sump 1" through-hull is filled in, and to evacuate water from that area a 500 GPH bilge pump is installed, either the automatic kind, or with a separate float switch. These are direct wired, with no switch, although I have added a transom mounted override switch to mine to avoid constant cycling is there is weight in the stern of boat while docked, etc, The water enters by back flowing into the boat though the two 3" evacuation drains.

The port side floor sump typically does not come with a bilge pump, but it is adviseable to add one, also direct wired with an override switch.

The two large 3" diameter splashwell drains and through-transom drains are to evacuate a large amount of water should it come into the boat, such as taking a large wae, etc. With the closed-in transom, there is no way to quickly get rid of this water, hence the large holes. In outboard cut transom models these are not needed, since the water can simply flow out the back over the transom.

In mine, the stern floor center bait well also came with a dash controlled areator pump and spray head unit, which have valves so it can do double duty to get rid of water that will flow into the well off the boat floor. If yours doens't have this, it should be re-installed, with or without the areator capability.