Seems like it has a single 235 gallon fuel tank (?)
Is the fuel tank leaking?

Here are some screen shots (below) from a factory tour video, not sure of what model year vintage these are from though . . . probably 2012-15 ish, but 2006 may be substantially the same.
Looks like the fuel tank runs in the mid-section of the boat up to the bulkhead that is under the center console doghouse. The tank is definitely installed before the deck assembly is joined to the hull. Also looks like the tank in bolted down to the main stringers along its length.
I would think that you would need to look to see if there is a removeable section of deck under the helm seat assembly leading up to the console doghouse. If not then it is a matter of removing the deck assembly/cap . . . or as you suggested cutting the cockpit sole/deck, which could be a bit tricky.
Maybe contact Mako to discuss . . .
