Both subs were getting the same signal (mono), the fronts are powered with a EP4000 and the rears are powered with an EP1500.
I solved the problem last night by running the rear sub line through one of the DCX2496 channels that I was not using, then running it through the FBQ and on to the amp. The DCX is very easy to use as far as the delay goes, the unit displays meters and milliseconds of delay, I think I ended up with a 7.?ms delay. Now the bass is nice and tight!
For music (2 channel) the 2 mains and the rear subs sound great, and the none of the speakers have been eq-ed yet. When the 2 mains with the front IB sub running the bass sounds a bit like one of those cars with the 30" wheels and a super matallic bass boat paint job. For movies all speakers with front and rear subs firing are pretty good, actually I can not tell if the rear subs are doing much of anything with the IB running.
So all is well for today, I probably won't start eq-ing anything until I get the rest of my sound absorbers up and carpet in.