Depends on the boat, but I am assuming if it is a cat, the subs will be mounted underneatch the deck and the mid/highs in the side consoles low?
If I had to do it over again and the boat would fit it, I would do the subs in the rear seat base (like Boatfloatings or Whipped565's)....much more bass too be heard. Also, I would mount the mid/highs as high as you can and not in the console...not sure if the boat allows.
In Xfactor's F26 he opted for custom made consoles (wood w/vinly) instead of the fiberglass where built in speaker locations were set up higher and angled towards the backseat...much better sound positioning then in the console aimed across the boat low.
If using quality componenets, I would say it more of your sound depends depends on speaker placement and less then components.
I would definitely look at the MB Quart head unit, or the Alpine if you want native IPOD integration..For amps, PG(Xenon), JL(Slash), and Zapco (Reference)...are lines I would consider..
For mids I would consider MB Quart, Focal, and Pierced....or another decent brand that makes something in a 7" or larger mid....For Sub's I really like the JLW6...just a great all around sub.
Well, that's a start...Good luck on the build up...