In my gigging days when I was using a home brew with a high gain preamp, I've put 2 tone stacks in the high gain channel.
It was built in my Fender 75 chassis, which was Fender's take on a MkIII Boogie.
I made it a lot more like the MkIII.
So the low gain and high gain preamp shared the regular Fender input stage - tone stack and vol controls (front panel) - 2nd stage.
The high gain circuit then took that signal via a gain control to a couple more cascaded stages, tone stack (back panel) and a channel master vol.
A relay were used to switch between the 2nd stage output and the high gain channel master vol.
This then fed an fx loop, reverb circuit, and power amp.
The second tone stack was simple, my own design, just facilitated variable amounts of boost to the treble and bass ranges, and was based on the treble and bass boost already in the 75; more aimed at fine tuning rather than a radical re-shaping.
I didn't want to use presence and resonance controls as I felt that they would mess with the regular Fender tone of the low gain channel.
To my mind, the 2nd tone stack was taking the place of the (optional) graphic eq of the Mk series, ie they allow the final tonality of the overdrive to be tweaked.
The regular 1st tone stack controls allowed the depth of overdrive in their frequency bands to be adjusted. So they eq'd the guitar to the overdrive, and the 2nd tone stack eq'd the overdrive to the fx (delay) / speaker / room.