Hi iWoofer,
Follow the steps provided below:
1. Connect the Yellow wire from the 4 pin connector that goes to the DVD ROM to from the SMPS to +12V and REM. Connect the black wire to GND.
2. Find the Green wire in 20/24 pin motherboard connector and short it with a black wire next to it. You either cut the green and a black wire and join them and if you want to use the SMPS in the system again then you can short them using a single strand wire in the connector itself.
3. Connect the power cable to the mains. The amplifier powers on when switch on. Please refer the manual on how to hookup the woofer to the amp. Revert if you have any doubts or issues.