The two sides of my dbx eq are completely independent of each other. I use one side in my Stiletto's effects loop, the other side with the microphone cable from my Banshee talkbox and into a PA.
I've used it with one side in front of the amp too, and it works well for that purpose. I don't see why you couldn't use it with two separate amps, unless there is a ground loop issue. This will vary from amp to amp, so you won't know until you try it.
I might reconfigure my rig, and use both sides of the eq in my effects loop. I use an Axess Electronics GRX4 switcher, so I can have two different eq curves and swap them in and out of the loop, giving my two completely different amp sounds with a tap of a midi pedal!