Setting up tones for a 2 guitar band is definitely a challenging task. Being the only Electric means you can dial in as a huge and phat of a tone as you want and you will be heard. With the two players, you need be very careful where you sit in the mix and having two distinct tones is actually beneficial. Generally, when I play in my metal band, we dial in very mid focused tones that are quite dry and we have individual rigs. My rhythm guitarist uses my old 2 channel Dual and I use his Mark V, both amps are generally EQ'd with a lot of midrange and the bass tamed quite a bit. Today, the rhythm guitarist was using my OD pedal to tighten up the recto and it helped out quite a bit.
With his Rhoads V with a Dimebucker in the bridge, he ran the OD with the volume up but with the tone down, but for his drop tuned 7 string, he turned up the tone quite a bit. I find that a Drop C# tuned 6 string is still quite mid focused but with a mahogany 7 string, it gets dark very quickly and the boost is almost required to keep things tight and focused.
I'm glad you figured out the 'resonance' thing. Usually, those low frequencies are awesome for bedroom playing or practicing, and work best live when they are shut off.