Hey Setter
I am redoing my system as well. Pretty much same stuff. With amps and what not. After researching on this site Kicker was where I went and always seemed to be offered as decent stuff that won't break the bank I did the 3 amp route. I am just going to build an amprack on the inside of my 2000 X-Star. Seems like it is pretty simple. All I am going to do is peel back the original carpet from the wall, add some material around the existing amp rack that came from the factory, and then recover it with the original carpet. Seems pretty simple if you ask me.
AS for the amps I did the kicker ZX650.4 for cabins, ZX450.2 for the towers and a ZX400.1 for my sub for the versatility. Each one of my amps will be run to an accessory switch on my dash so it can be individually turned on and off. I have a wife and 2 young daughters (1yr and 3yr) that are on the boat more often then just me and my buddies. So they are not into the sub and blasting the cabins while I ride. So I wanted to hear the tunes while I ride but not blow them out as that was the only way the "boss" would approve tower speakers
. But then when I am out with my buddies it is game on. Also could have faded the stuff like you say, but I like the idea that if the speakers ain't running the amp isn't pulling power. Just my own thing I guess. Good luck with your system. Can't help you with the amp overheating thing as I am not that stereo savvy. Just went with some good advice I got from friends and acquaintances here.