Sound engineer here - not a guitarist. Spent a bunch of time with my son's Cat 60 for exactly this issue. Line level too hot & clipping coming out of the amp - regardless of the desk gain-staging. Here's some notes I hope some will find helpful.
Master Volume knob (as mentioned above) has no bearing on Line-level XLR out.
As you'd expect, channel gain, boost and channel volume all DO have an effect on Line level out. What isn't intuitive is that you can easily cause the line-out to clip without it being audible through the cabinet speaker. This is a bit of a shame, since you can't just set-up and save your sounds using the cabinet and your ears - you need to connect to the desk and set-up your preset sounds whilst monitoring both. Desk with headphones helped me to be the most precise.
I found that with my son's guitar & the gain/boost set to give a decent clean/dirty sound, setting the channel volume higher than 40% would clip the line out if you hit the strings hard. I typically ask players to keep their guitars at full or close to full volume to get the best S2N ratio and to avoid surprises mid-gig, but guitars have different max volume outputs depending on the pick-up and electronics. So you'll need to experiment with yours at full volume to see typically where your XLR line-out clips.
I found that some of the standard presets - as shipped, even after factory reset and firmware update - clipped the XLR Line output. I needed to reduce the channel gain/volume on each preset and re-save each preset - then run the master volume a little higher afterwards to get the same relative volume from the cabinet. It's all solveable with 30 mins playing about - but Line 6 screwed up their factory set-up IMO.
Worth noting that each preset - when you recall it - recalls the gain, boost and channel volume (+ all parameters) that you saved it with. Thus, although all the knobs physically stay in the same place when you recall a preset, most of them will have moved virtually - with each preset recall. Once you move a knob, it recalibrates that specific parameter to match that physical knob setting, but this isn't obvious. The Fender Mustang amps have an visual to show this on the display but the Line 6 doesn't - it's far from intuitive.
The best way to visualise all this is to use the Catalyst app on a PC or phone and connect to the amp with USB cable. Then you can see on the screen once you change presets what is actually happening - this is when it all made sense to me. I was able to edit & re-save all of the presets with the amp speaker off, using headphones through the desk.
Strangely - and this may be in the manual but I couldn't find it - if you have phantom power (+48V) on at the desk, this reduces the line level output of the amp. Some kind of auto-sense between line (off) and mic (+48V) outputs? Ironically, it didn't change where/how the line output clipped, but with +48V a) there was a load more hiss on the amp line-out and b) the line-out volume was lower. Cabinet speaker unaffected.
Bottom line - if you're experiencing this clipping and your desk is set right, you'll need to re-save the amp gain-staging for each preset and it's much easier to do this via the Catalyst app.
