I'm horrible at explaining stuff.
The current hole that drains the inner bottom to the bilge will need to be enlarged but big enough to act as a drain hole also with the hose and wires running through it. Or you could simply drill a large enough hole above it to accommodate the hose and wire for the pump.
I don't suggest through the transom, either side just below the rub rail would be easier.
See this thread, note the bilge hose location.
http://www.wellcraftv20.com/communit...=battery+bilge