Sub Amp fading out issue ?

I have an issue with my stereo system, not sure how to overcome it. I'm running 2 amps, 1 amp for highs and 1 amp for sub. Both amps run on there own dedicated battery with a battery share switch. Other battery runs the boat. Did this so I can play my stereo while swimming and not worry about draining my starting battery. Now, what is happening is after we sit for a while, the amps are getting hot from cranking it up. I had no choice but to put the amps in the rear engine compartment and I think that's my issue. The engine is getting these amps pretty warm, plus jamming them out. Once they get hot, when the sub hits, the stereo starts fading out. If I turn the gain down on the sub amp, everything is fine. The sub amp seems to be the hottest. Is there a good way to cool these amps or do I need to try and relocate the sub amp under the dash on sub box perhaps ?