His writing style may not be for everyone, but this is an absolute goldmine of information, and the impetus for the whole thing was how to deal with large volume swings on "chugs" on the guitars.
Slipperman's Recording Distorted Guitars From Hell
Any number of potential issues and solutions to your problem, most of which you can find in that link, but you might want to start by rolling off the bass on either your amp/modeler or simply high-passing your guitars and letting the bass do the dirty work. This isn't a Recto model you're using by chance is it? Those things (as a Recto owner myself) have so much low end in Modern mode that you really DON'T want much bass at the amp - for leads mine's usually at 0, and for rhythm generally under 9 o'clock.