batteries are best to be kept in the the transom area. ive never seen a battery in the front of a boat, but you can be the first.
remember that a boat is not like a car, so you are not powering lights, a/c units, ect. unless you have a beast of a motor, one alternator and one battery should be fine. i would suggest you adding an additional battery with a perco or isolating switch, for that extra protection of killing battery #1. i would suggest trying one lower based amp for your subs and not connecting any amps to the mids and see how you like it from there. you are very limited on adding a bass thumping/sound speaker system in a 18ft jet boat. it will not sound anything like a car, because its a boat with open space. i had a little day cruiser with 2 12s and some extra mids and it sounded ok. i put that same set up in my car and it sounded a lot better. the boat system would sound better if you dynamat the sides and floors and put the subs in a fiberglass enclosure. thats just adding pounds of weight and would definately affect the handling/weight of the boat.
example; when your sitting in the drivers seat of your 2 dr honda civic, the stereo sounds good. now open your trunk and stand 5 feet away on the curb. it sounds like a rattle can of crap.
easy scenario would be hook up a amp to the 2 subs, have a good head unit with atleast 200 watts per channel and a set of good 4-way mids. that should be simple enough to sound good.
enough of me rambling.