I've been using NMV Marshalls or the last 7 or 8 years and here are a few things I do which you could try.
This is based around a Les Paul style control knob configuration so some of it may not work as with other guitars. Also note that I run a Marshall super bass version of the 100 watt head and the bright channel input is where the awesome is at, which is fortunate, as it doesn't seem to like bridging the inputs. Unlike my old 1959 super lead which was ALL ABOUT bridging the channels and mixing the tone.
First thing I do is set a base line rhythm crunch tone. I set the guitar volume and tone controls to 5 and then dial in a sound I like at the amp. It should give me nice picking dynamics so it 'cleans' up when I play lighter and starts to growl if I dig in a bit.
A lot of guys say no no you can't turn down an LP without the tops rolling off but in this case that's exactly the best thing. If the sound is sweet at the amp then when you turn up the guitar, the tops are gonna jump out a lot more and give that lead break boost and cut through.
The other thing I can then do is use a clean boost pedal (leave the guitar rolled off) to get that quick volume push when the pedal is in. Sounds awesome.
Another trick I saw which I like to use a lot is to roll the bridge pu volume off just a touch and roll the neck volume almost all the way down. When you set the guitar to the middle position it cleans up heaps but keeps the basic tone of the bridge pu. You can tweak the clean/dirty mix with the neck pu volume. When it's time to get all grindy, just flick the switch to the lead pu and there's all your volume boost and tone. Easy to flick back to the middle or neck pu for sweeter clean tones. It works like three channels in a way.
caveat. I like a sort of messy break up from my amps so this isn't super precise and you sometimes need to adjust your playing to contain feedback. But that modulation and volume control hopping is what these amps are all about I reckon.