Cap's not gonna help, it's in the wrong place in the lineup...caps are for supplementing the draw from battery to amp when the amp asks for too much. If your HU is indeed the problem, and your batteries are all charged up (and staying that way), you might just want to try recalibrating the HU so that you're not turning it up as far...are you running and speakers off the HU at all? If not, see if the HU has a way to disable the internal amplifier entirely, I don't run anything off mine, but there's no way to disable it and it still heats up like a mother, which i hate...My next one will have a way to send the 5v RCA signal to external power only.
At any rate, how's the HU tuned? Do you have it to where you can turn it all the way up? Typically this is the best way, but if your HU is starting to go, it might not like it much anymore...
Check your batteries first though, make sure they're still holding power. If not, replace them both, and make the 2 new ones identical. Hope that helps a bit.