Hello jason_dil,
Having 1 channel go out is a common problem with audio systems. Unfortunately, since it can be caused by faults in the wiring, head unit, amp, or the speakers themselves, it is tedious to troubleshoot. Being tedious doesn't mean that it is difficult. You can do it with a little planning and organization.
Here's a link to www.caraudiohelp.com/help which has pages and pages of step-by-step troubleshooting. I recommend that you read up just a little and print out any of the guides you need.

What you want to do is eliminate what ISN'T causing the problem and isolate what is.

1) First, do a physical check of all the wiring. Make sure all connections are secure and tight and that there are no obvious cuts, tears, or breaks in the insulation. Check all fuses. Either replace them with known good fuses or remove and check with a meter. Check RCA's plugs on both ends. Remove and reseat each plug. Make sure the pin is not broken off inside.
2) Move on to the defective sub and it's wiring: See if it works on the other channel.
3) Check the head unit output: Reverse the channels of the RCA's and see if the problem switches to the other sub.
4) If everything checks out in 1-3 above, you've isolated the problem to the amp itself. It probably has a faulty component and will need to be repaired or replaced.
Hope this helps. If it does, please rate as "FixYa". Thanks!