One option you may want to consider that would let you keep your old deck is getting something like the Exile Audio Zone Controller Preamp. This lets you control the volume levels of all 3 zones independently: sub in-boat and tower, and it gives you a Aux input you can connect your media player to. You would need a Amp to drive each zone and not use the existing deck to drive a zone like your in-boats.
Wetsounds also has something similar I believe.
In my boat a 07 21V, we replaced the Oem sub with a custom built sealed enclosure and moved the heater forward. Amp wise you probably want a dedicated amp for your tower speakers and if you want to save money get a 5 channel amp to drive your sub and in-boat speakers instead of a separate amp for those zones. Exile has a new 5 channel Javelin amp not sure that meets your budget constraints.