Alot has to do with the boat itself. Like my old boat was an outboard which only gives back to the battery what it uses, meaning stereo's, lights, etc, drain it.
Withthe new boat its a sterndrive, and it has a 65 amp alternator that puts out 14.4 volts at idle, so a single battery can get re-charged.
Now on a boat it is always the best idea to have two batteries, just in case. Personally I run a single Optima marine deep cycle and keep an eye on the voltage. For extended trips I always bring a back up (not int he boat) and my jumper box for those day trips.
Now it also has a lot to do with your boat as to where you put the sub and what kind of sub to use.
I am installing a single Rockford 12" in my boat in a band pass enclosure. It will be mounted under the dash in a compartment where it will likely never get wet, but since it is a bandpass the speaker is completely inside the box and water will only splash on the box which is fine with me..........
Many boats have a ground distribution block like mentioned above and you want to wire the amp to that, straight to the battery if you dont have a ground distribution. On my new boat it has an accessory spot in teh circuit breaker panel, and a ground dist block back near the battery, so the + feed will come from the factory circuit breaker panel and the ground will go back to the dist block.........
Keeping the amp as close as possible to the battery is your best betm but thats not always possible.
Also remember a sub or speakers can serisously screw with a compass, so check that before installing........also use stainless harware on everything so it doesnt rust......
Oh and boat marine audio is usually cheaper then car stuff! so shop around, I got everything for my boat for under $500 including a face off MP3 Excelon deck, 12" Rockford punch, MTX 4 channel amp, and Jensen marine speakers........