Ya D..if you are auditioning the factory patches on there...most of those were never tweaked to adjust to some of the firmware updates which changed things like the compressor, drive, etc.. I never loaded the updated factory patches released with 8.xx...I'd assume that would address the level issues.
The amp level output is the most obvious place to start, but that's going to vary with how hard you are hitting the front of the amp block with compressors, drives, etc so you might have to start with reducing some of those up front levels first if they happened to have gotten jacked up in a firmware change.
The output 2 knob on the front isn't going to have any impact.
If you haven't done it yet, just build your own patch from scratch for practice. You'll have o problems getting a good strong level without clipping. The key is to audition the patch with the various effects bypassed and active, and try to adjust the levels so nothing boosts the signal too much when it's engage (unless you are going for a boost effect of course). Noon on all the levels is always a safe bet to start with

. Or a straight amp/cab patch would be pretty easy to identify problem areas!
Also, with the QSC, I'd recommend increasing the low cut parameter in the advanced amp page...that is, unless you like massive, booming bottom end. Got nothing to do with the internal clipping, just a tip for building your own patches.
Hope you are enjoying!