you are correct in just swapping out the speakers on the tower and the boat. make sure that all the wiring is intact, good quality, series/parallel is correct and polarity is correct.
as for wiring a sub, there are a lot of good threads here on where to place it. wiring is simply running the cable from the amp to the sub.

in your situation, personally, I would look at upgrading the 4ch kicker to a 5ch. use 2channels for the 4 cabin, 2 channels for the bow and then a single channel for for the sub. with the right amp, you won't need to run a dedicated sub channel. nice to have for balance and fading, but not necessary. or you can add a 3rd amp to power the sub.

once you decide what route to take and what/where to place the sub, you can get into more specific questions.