It doesn't take much to over-amp a deck.
You'll thermal your deck if the resistance on your speakers are too high, if the feed is too hot, or if the feed is too cold, and it has to work in-efficiently. The best thing I can tell you to do is this:
A.) Mark your wires. (Hopefully they're already marked in the harness for your deck.)
B.) Disconnect your harness, and check the resistance across each set of speakers.
c.) Check the Amperage coming in your ignition power wire. It should be a little lower than the fuse numbers.
D.) Check the resistance of the ground wire/solidity of the grounding points.
If everything seems to be in line on the hard side, then you have another round of testing.
There is an audio test CD out there that rotates frequencies and gain points, they're usually used to test the quality of high-end sound systems. Use the CD and a stopwatch, and a piece of paper to track the time played, volume setting, and general area of frequencies that cause the problem.
*Warning: You were just taught how to build a watch, since you asked what the time was.