Didnt follow if you where going to be using a head unit or not, but if you do, you can use your fader on the head to control distrubution of music. Thus, if you where to hook your tower speakers up to one amp, then using your RCA's plug that amp into the rear output of your head, and also did the same but opposite to the interior speakers. Using the fader, u can distrubute your music where more is headed to the tower, and less to the interior.
Use in inline RCA bass remote. Which is what wetsounds has clearly constructed. Then you can indpendently control the amount of volume to each area.
IMHO - I am reworking my system in my boat as well, and will be using the first method. If this does not work, the RCA bass remotes are only 20 bucks, I will be switching to those. I just want to see if the fader will work without having to put additional holes in my dash for these remotes to sit.