I need help.

I have a decent knowledge of electronics, but have never attempted any mods with my boat stereo.
My current setup is:
Kenwood HU (stock)
2 Kicker Amps(2 and 4 channel). One runs the boat and the other runs the tower.
Tower speakers (PolK)
Boat Component Speakers (stock)

I just purchased 3 sets of the Polks from Amazon. I will be replacing the components. I assume that is pretty simple.

I will be purchasing the Kicker KMT6's for the tower. Again, I assume this will be basic, just swapping out what I have.

I would like to add a sub(suggestions?). Here is what I assume will be the biggest issue. In addition to the sub, I will be buying a new head unit. It will most likely be a Kenwood so the remote will work. It will also have a sub output.

I would like to wire the sub so it works for both the tower and boat. Can I run it directly from the HU or will it have to go through an Amp? If it goes through an Amp will it work for both?
Also, how complicated is the wiring/powering of the sub?