Sounds like that is the other GPU plug, then.
This cooler should work well for you:
Newegg.com - Rosewill RCX-ZAIO-92 92mm Sleeve Bearing Fan CPU Cooler
I had an Artic Cooler version with the same basic design that worked very well. Again, mount the cooler before mounting the mobo as it is much easier to do it that way.
When mounting an AMD cooler, hook the non-clip side, try to center the cooler over the CPU, make sure the clip is in the non-locked position. It will take a little force to push the clip side down and over the knobs/hooks, but not an awful lot. Once they are over the hooks just lock the latch.
This video should help: