the subwoofer (connected through loop out)
This is your problem. What you want is pre-out or sub out. Loop is fixed line level. Essentially a bypass, it gives no volume control over the sub. Because of this it is simply playing way too loud.
Your amp does not have pre or sub out. The solution is a $20 Line Out Converter. You might be able to find one at Parts Express for even less. Don't pay more, it does no good. Connect the LOC to your speaker terminals on the amp, then connect your RCA interconnects from the LOC to the sub.