thru hull location

In the final planning stage for my ballast system on the Cobalt. Gonna use 2 Jabsco pumps to fill 4 bags. My problem is where to put the thru hull. If I place it on the bottom, I can fill on the fly. But getting the right spot so it doesnt interfere with the padded bunks is going to be a PITA. If I place the thru hull on the transom, I should still be able to fill while putting around right? I realize I wont be able to fill on plane, but if I can fill while putting around I would be OK with that. Plumbing it from the transom will be much easier as well. Thoughts?