I just pulled up the V-Twin manual...http://www.mesaboogie.com/manuals/V-Twin%20Rack%20PreAmp.pdf
, as I couldn't remember exactly whether the Presence controls were boosts or attenuators. I had to read quickly because I"m misappropriating work time.
My methods for tuning an amp involve changing only one parameter at a time. The Masters (either on the power amp, or the pre) should only lower volume. Personal experience (to my ear) leads me to believe that they also change tone in minor ways. The most powerful control is the Gain. By opening up the Master on the Preamp (Wyde-Clyde is like Dimed, or Cranked), any attenuation of signal should be eliminaed. Same with the Presence. My sense is that you'll have to barely crack the volume on the power amp, or you'll be removing paint from your walls.
So...Eliminate any secondary or tertiary attenuation. Presence and/or Master. Send the Mix to the Clean Channel, and adjust the tone stack. Then (if you can bear it) bring the gain up till it's just "there." Everyone hears Jerry from a different era in their own personal Head. Now you can pull remaining ice-pickyness with minor adjustments to Presence. At some point, just try the Master. Once you understand the other tone controls, you'll use this to tame the beast volume wise.
Once you've got the dynamics in the preamp to your liking, start playing with the Presence on the Power Amp.
This is an incredibly sophisticated setup. I've loved all the Mesa gear I've own, and I'm playing almost exclusively GD.
Be patient. Read the manual at a leisurely pace. Your playing sounds great, so have a great time grabbing the tone you want.
Hope this helps.