I apologize if I'm stating the obvious, but the first thing one should do when setting up a bi-amping configuration is to put one of the bass amps on, say, the left speaker and one of the M/T amps on the right speaker. Drive each speaker full range and adjust the left/right level to get a reasonably close balance. Check if the relative L/R polarity is in phase or out of phase-- a strong center image or a diffuse extremely far left, far right sound.
If you get a solid center image, then you're good to go for bi-amping. Otherwise, you'll need to connect the bass amp and M/T amp in opposite polarity when you bi-amp, since the test showed one of the amps inverts polarity relative to the other.
If you don't test the relative polarity of the amps and connect them so the bass amp is out of phase with the M/T amp, you may not get a horribly out of phase sounding result, but the two amps will null the frequencies where they overlap, causing a terrible mid-bass hole in the frequency response.
Again, I'm sure everyone checks this before bi-amping, so sorry for stating the obvious.
Robert