What pump are you using for the skimmer, and is it in sump or external? If it's in sump, does your sump level fluctuate?

Personally I'm not a real fan of aquaC skimmers, but I bet you can get it set up so that it doesn't go too nuts. The overflow into the sump is a really good idea; either a fancy waste container or just the jug in the sump works great.