The electrical brains are located behind the driver's kick panel so installing a sub there is going to require more than most of us are willing to do, although it probably can be moved. I am as crazy as the next guy, but screwing with all those wires seems overwhelming.
Do you have any pics of that? I cannot imagine getting 2 12 inch subs in there. There was a guy on team talk who actually put the pieces of the box in there one at a time and built the sub box inside the compartment, because once built, you can't get it out, and there is not enough space to slide a single box in there. Maybe it just slid in that compartment under the seat next to the side of the hull?