EDIT: see my post on Page 3 - after some extreme testing, I do not believe the EQ's were clipping. I think I was creeping into Output clipping without realizing it. There may be some additional weirdness going on, but I was not able to replicate my initial issue while keeping my output levels clearly in the "safe" zone.
I have a couple patches rigs where I am using a few Studio EQ's (one patch rig has 4). I know how everyone says "try to make cuts only". Yeah, yeah, I know. But if EQ's weren't meant to boost ever, there would be no option to boost. Anyway, I found my tone was getting a bit harsher than it should be, particularly on the high strings in the middle of the neck. At first I thought it was the profile and started adjusting EQ to compensate - reducing the highs around 3 kHZ to get less crackly breakup. This helped a little but I was still left unsatisfied - something else must be going on.
I remembered another patch got nasty because I had a chain of Distortion and Compressor where they were both boosting volume and it sounded terrible. I forget which one was the offender, but the problem was that the first effect had a big volume boost going into the second, and the second did NOT like it. Once I turned the volume parameter down, the tone cleaned up and sounded smooth and natural again.
I tried the same approach with the EQ's - reduce the volume parameter of any EQ that feeds another EQ. Voila. Tone completely cleaned up. EDIT: this was probably due to lowering the output levels, not due to the EQ's. I did tweak to compensate for that initially, but I probably didn't tweak to match the initial output level.
Another thing that helps is if you are ever daisy chaining EQ's, make sure the first one has your cuts. If you have to boost there, only do your mildest boost.
A good setup is Graphic EQ (easy to maintain the sound you want with cuts only) into Studio EQ (to use the parametrics to boost/cut those specific areas that need work still).
"Why so many EQ's?" Because I like to party. No, actually I find EQ'ing is the crux of a good distortion tone. Normally, people use OD stomps or boosts to pre-eq their tone. This works great, but these units/models often do more than simple EQ. In some cases that's good, but sometimes it changes the tone too much. Also, their EQ'ing abilities are usually quite limited in comparison to the dedicated EQ blocks. On the other end of the spectrum (post-eq), bass, mids, treb, presence are great, but often not enough for me. I like bass but not boominess, treble and presence but not fizz. You want to lop off the ultra-high and low end, you're going to need one of the dedicated EQ's. And sometimes you want to get "between" those BMTP controls, or make boosts/cuts that are narrower or wider.
Don't fear the EQ. Just know the pitfalls.