Ok, sounds like you have a Tige with the factory ballast, which should already have the EIDB dual battery system as it comes standard with Tiges with ballast or heater or tower of power stereo or tower lights or any combo of those options. If the boat does have the factory dual battery setup, there is a diode Iso that will need to be pulled out of the loop.
If it were me, I would pull the factory rear ballast tanks and move the battery(s) back against the transom like it is in the non-ballast Tiges. If it doesnt have factory ballast, then not sure why your are needing to relocate the battery(s).
Amp rack: No need unless you want to go all out on custom work. The pass side walk-thru wall has a composite board glassed in that is apx 1.25" thick. It's plenty strong and large enough to hold 3 amps. I like to pull the cooler and pop my power cable through the bulk-head wall separating the cooler area and the storage.
Sub: I'm guessing you're going with a 12" of some kind and will be needing an enclosure. The drivers foot-well wall is a great place for a sub. If you remove the front seatback lift support, a box of the proper volume can be squeezed in to the storage opening, but I recommend mocking it up in cardboard first, just to make sure it fits.
Does the tower currently have speakers? If were done factory (or at least the tower was factory pre-wired) it will have two pulls of 12ga. If you need 4 pulls, you will need to pull the 2 12ga's out and pull in 4 14ga's, 4 12ga's wont fit. The tower wire can be run down the tower tubes and through the port side gunewale, so it will be completely hidden. For the lights, take the wires down the starboard side with the nav light wires.
The Enzo sac is a perfect fit for the 24Ve. A custom will cost just about as much, plus the enzo already has extra valves for filling/draining.
Like Ajholt said, do a search on TO's.com, i've posted lots of pics on fishing the tower.