What year/model is your boat? A lot of the newer boats that came with towers are pre-wired. To keep water out, just drill on the bottom side of the tubing up by where the speakers will be mounted. Does your tower have pivot points to allow you to fold it down? What tower is it?
I just rewired my 06 rad-a-cage yesterday with 4 sets of 12 guage wire. I used the old wire that was already in there to pull the new stuff through. It was not an easy task, so expect it to take a while. One thing that helps a lot is to lube up the wire with some dish soap. That made a world of difference for me.
-Mike
2006 Supra Sunsport 20V