Are you getting any distortion or feedback when you get the clip notifications? If everything sounds good but you still see the notifications, I'd suggest leaving it as is.
If you are experiencing distortion or feedback, I'd suggest taking Master Gain down a bit further.
The CPT2 preamp can be VERY hot and is prone to feedback and clipping. I've seen other users have to drop Master Gain down to 5-10%.
It may also be worth setting the high and low EQ sliders right in the middle as well.