Steve-
Car and boat stereos are more similar than different. The major difference is the boat's lack of a great big metal frame/chassis to supply a super-good ground as Hangar Pilot shares. Your amp grounds have to go all the way to the battery.
The lack of a ground plane also has caused us to come up with some different schemes for getting rid of noise. The most common and repeatable thing I have discovered is that wiring the radio power to the amp, (or the largest amp in multiple amp installs) power terminals. This provides a good COMMON source of both 12 volt positive power AND ground for both the amp and the head unit. This prevents the slight difference in ground potential that is the root cause of most boat stereo noise. I have provided the simplest examples of this sort of wiring mod:
In this first picture, we are using a simple dash rocker switch to turn the radio on and off. This is absolutely the simplest wiring.
This second pic shows the use of a 30A automotive-style relay. The key's accessory switching provides a trigger signal to the relay, and the relay in turns energizes, sending power from the positive amp terminal to the head unit.
Study these a while, they really are simple, and don't be afraid to try it. I do this now for every boat system, and I still will often print out a copy and take it out to the boat I am working on, just so I can see it...
Wiring the speakers to the amp is for all practical purposes the same as on a car. Just take lots of extra care with the wire and any pinch points or abrasion points, you do not want to accidentally cut the wire or abrade it to a short circuit in the tower or at a point it goes into the tower. OTHER folks have some awesome recommendations on how to actually pull the wire through the tower. Hopefully those guys will chime in with the tricks and techniques that have worked well for them. TigeMike is one guy who I know has a lot of experience pulling tower speaker wire; hopefully he will chime in!
Good luck and let us know!
Phil
Kicker