the output clip light should never come on. this is different from the INPUT meters, where an occasional clip is ok. output clipping actually loses data. (i think there is a bit of headroom, but they really shouldn't ever clip.)
simply turn down the amp level on the patch that clips. you may have to adjust your other patches down that much too.
the output knobs on the front panel do not affect output clipping, they only control the total level coming out of the axe and supplied to the next thing in the signal path. again, the clipping is due to the levels in the blocks in your preset.