If you use the M2Lead, or Recto amps, dial the knobs to 4 or lower & go from there. Epecially on the M2, I leave the gain on 1 or 2 half the time with my Tonezone pickup. Most of these amps were made for low output pickups. Going from a Peavey Wolfgang (low output) and a Schecter with Duncan Distortions (hi) meant that I had to start from scratch again. Not a lot of my presets sound right with my Tonezone now, but I usually am dealing with the same EQ frequencies I always have been, and simply have to adjust them up or down depending on the EQ curve of my pickups.
After you find your gain starting to break up, try the JRC and just use it for a mid boost, keep the gain and levels down to 3.
Step 3, and maybe even 4 is to EQ your way to your tone. Don't try and pick a mic and put it off axis to get there. Use the setup you would normally use, even if it sounds like a buzzy fizzfest at first.
Step 4: My first EQ is usually a bump in speaker simulating frequencies around 350 Hz with a wide band, sometimes 400 with a narrow band helps solidify the sound. If it's still boomy, you may need to set up a highpass filter, so keep the first paremetric EQ setting untouched as you play around with low mids. What you are doing is bumping frequencies so that the noisy ones are a bit lower, but not just notching them out. You can still do that at the end of the paremtric EQ by using a low pass filter and playing around with the bandwidth, which will become the rolloff.
The next few frequencies yo want to check out are 750/800Hz, 2000/2200Hz, 2700/2800Hz, 4kHz, 6kHz may be your low pass filter, or even 4kHz...but test different ones and use the bandwidth knob to roll off.
Derfinitely set up a reamp session and record yourself playing when you get something usable, then you can freely work on making changes as it's reamping again.
Get something that feels and sounds good to you, save that, then try and tone match and save that one also.