It depends on the gain set-up of the amp.

If channels 1 and 2 use a gain, and channels 3 and 4 use a seperate gain, there is no (easy) way to tell the the gains are set 100% identical. If they are on seperate gains, and channels 1/2 is set at (say) 50% gain, and channels 3/4 is set at (say) 55% gain, the the 2 woofers will move differently. ONLY slightly, but enought to definately alter the sound (how much?? Not sure), and possibly harm the woofers. With a voltmeter and some knowledge you can get the gains close. With an osciliscope, you can get a LOT closer.

With all THAT said, just make seperate chambers for the 2 woofers....save some effort. OR, you could get an amp better suited to run woofers....