If they're passthrough connections then no, your should should remain the same regardless of the cabling schema that you decide on, but like the guy above said, you're limited in your adjustment of your onstage volume as a result, unless you manually adjust via the gain control on the back of the CLR.
You're much better off dedicating one output to FoH, so you can set and forget your level there, use the 2nd set of outputs for onstage monitoring so you can adjust if needed.
Then again, assuming my sound guy is competent, I'm pretty strict about 'don't touch amp volume during the show', so there's that to keep in mind.