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The master volume won't change the clipping in the input/output so you can leave that where ever it is. This is what I would do. Check clean and distortion settings press the input button. I'd put the Distortion sense at zero and see if that changes the input LED from going red. If it does all is OK. I'd then go and check the clean sense make sure its at zero does it clip when you play a clean profile. If it does I'd lower the rig volume.
I use an American PRS Navarro modal which has high output pickups. My clean and distortion sense are set both to 0 and to stop clipping I turn the rig volumes down to around about 10 'o' clock
Hope this helps you
Hey Raoul,
My Kemper is set to "0" for the Distortion sense and "5" for Clean sense (I think those are the default values, aren't they?). It seems that if I roll back the clean sense there is no clipping but it also changes the tone dramatically in a negative manner. So based on that, is there something else I should try besides adjusting the clean sense? I'd love to keep the tone the same just minus the clipping. 
Just as an FYI, I'm using the "Sultan" profile which I believe is one of the stock profiles. Sounds fantastic for cleans but with the clipping it's killing me. 
I'm struggling a little bit with the Input/Output LEDs on the face of the Kemper and I'm trying to understand what I need to change to solve my current clipping issues. 
I'm playing several different guitars equipped with anything from single coils to humbuckers and it seems like it's not specific to the general pickup output or anything like that, especially since one guitar in particular (PRS NF3) has pickups that aren't crazy hot, yet it clips the most out of all my guitars and it does so in almost any pickup position. I tried lowering the pickups to see if that was part of it and it doesn't seem to have helped the issue, plus I'm still getting the issue on other guitars as well. If I hit single notes or chords with even a decent amount of force on some of my guitars, the input LED flashes red briefly (which I thought was normal and why I didn't mess with the clean/distortion sensing settings, right? 
), but the Output LED flashes red and I get audible clipping through the speaker in my FRFR cabinet! 
I tried lowering the volume knob (master volume on the right side of the Kemper) to see if that helped and it did a little bit but not a ton (I don't recall what I was running it at previously, it's at noon on the Kemper now and I can't remember if that's how I had it set up or if that was something my friend tweaked the other day come to think of it... hmmm... 
). Should I lower the master volume further (so running volume on the Kemper at somewhere between 9 and noon on the dial) and raise the volume on my FRFR cabinet instead? I don't remember how I had it set up before he was tweaking things as we were A/B'ing FRFR cabinets and he had changed stuff from how I had it set up previously and now I'm almost wondering if that's part of this whole issue. 
Hopefully it's just a volume change I need to make between the master on the Kemper and the FRFR, because I didn't have ANY clipping issues when I first got it and now it seems like guitars that were fine previously are clipping as well so I'm starting to think maybe it's not the guitar itself.... 
HELP! 
LOVE IT! 
I play metal primarily so for me, while I've found a ton I love already that I didn't have to pay a dime for, I consider that a lucky bonus. I don't mind paying a dude for his effort if he's taken the time to put together some killer sounding profiles using high-end equipment to do it!