You may just need to adjust the jumper settings on the board. I know there is a time delay before the PSU will shut down the computer. Look it up in the manual, i know that is how the M1-ATX works.
As for the remote turn on, i believe that isnt used to POWER the amp but rather act as athe remote power line. There should be a seperate power line to the amps, the remote line will then just turn the amps on.
If this is what you are doing, maybe the amps need more power to the remote line. In that case, the psu can turn on a relay that then directs 12v from the battery to turn on the amps, achieving the same goal.