The high pass filter for channels 1 and 2 is set at 50Hz by the look of it (though I can't see the low mark on the dial). It should be the value at which the sub's low pass filter is set, which for some gay reason looks to be 150Hz. This should be more like 80-100Hz (to start with). Otherwise your fronts are trying to play very low bass tones in addition to your sub, and your sub shouldn't be playing up to 150Hz.
Your 'mode' switches are set correctly.
The outputs are wired correctly.
Start by setting the low pass value vertical at 100Hz and set the high pass filter to be the same (turn it clockwise until it's at about 100Hz). If you have a digital crossover on your head unit, use this instead and set both pass filters to be 'flat'.
1. Turn phase and bass boost all the way down to zero, which it looks like they are.
2. Turn the level (gain) down to zero on front and rears.
3. Make sure the input sensitivity switches are not selected, i.e. at their outermost position. This is only an attenuator used to bring pieces of the system in line with each other. It basically determines whether or not to reduce the strength of the input signal, which you don't want to do. It looks like both of these are correct.
4. Turn head unit volume up to 75% of maximum.
5. Using a typical CD, increase front and rear gains independently (marked 'level' on your amp) until they're as loud as you'd want them. If you need to go beyond 25% gain or so, increase the input sensitivity until it is loud enough.
6. See if it sounds ok.
If the amp is no longer overheating, there must have been a problem with the rear speakers. I suggest getting the rears connected to the head unit's rear channels, as many others have.
The remark about the problem being due to the quality of the music on your iPod is one of the most stupid things I have ever heard.