Have you tried gain matching each subwoofer? What you have to do is start with one subwoofer in one fixed location (with crossover 'Out', bass extension switch in the down position, phase '0', volume knob 1/4 of the way up). Set your A/V receiver master volume level to a moderate level that you would normally use during music playback. Place the sound level meter at a fixed location (say, 1 foot away from the front of the subwoofer?). Play track 14 on the Test CD. Write down the SPL that is shown on the meter. Then move out the first subwoofer and put the second subwoofer in the exact same location as the first subwoofer. Set everything the same on the subwoofer amplifier (with Q = 0.7 on the VTF-3 MK4), and adjust the volume knob until the sound pressure level is the same as the first subwoofer when playing track 14 on the Test CD.
Then you can move each subwoofer into place.
Note that you may have to reduce the subwoofer channel level on your A/V receiver. When using two subwoofers, the combined level will generally be ~ 3-6dB higher than a single subwoofer, so you can adjust the subwoofer channel level on the A/V receiver to compensate.
Do make sure that each subwoofer is in phase with each other (ie. when you play one subwoofer and then turn on the second subwoofer, then sound pressure level should increase rather than decrease). Then you can flip the phase switch on both units to see if the subwoofers are in phase with the main speakers.
Pete - Hsu Research