The way I read the OP was that they have two different amps they want to use with the 11R. In my head they have a Fender amp and a Marshall amp (because that's what I think of when I think clean and gain). My interpretation was that they wanted their clean presets to go to the Fender amp and the gain presets to go to the Marshall amp.
My solution is run Output To Amp 1 to the Fender and Output To Amp 2 to the Marshall (regardless of whether you run to the Effects Return of the amp or to the input).
On your clean presets you set the Output To Amp 1 level at whatever your desired output is and have Output To Amp 2 on MUTE. You do the opposite for the gain presets.
If you want to get completely crazy you can also blend the two. =)
I don't know if that was the actual intent of the thread to begin with, but that was how I interpreted it and what my response was based on.
That said - it's entirely possible I missed the boat completely! :-)
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Guitars:
Strat PartsCasters (x2), 81 Ibanez Artist, 2012 Gibson Les Paul Studio, Epiphone ES-339 P-90 Pro
Effects:
Atomic AmpliFIRE, Avid 11R, Franklin ProDrive, Franklin F-Plex Delay, Line 6 M9
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