I have the same boat. Do you have the roswell towers?

This is the order i would work in ...

1. Tower speakers. This will also require 1 or 2 amps depending on how big you want to go. They make 6.5" direct drop in for the roswell speaker/light. HLCD or coaxial.

2. Sub. The excelon they put in the boat is a pretty good sub and DVC i think. Biggest thing here is a box and proper amp. You can have a dedicated amp or use a multichannel in line with the in boats.

3. In boat. Biggest thing here is doing the wiring properly as SC f'ed this all up.

4. I didnt bother replacing my head unit. That kenwood head unit has an aux input that you can buy the dataport for apple or run rca to plug into a headphone jack.

Purchase amps in line with the speakers so you can match up wattages.