The others pretty much summed things up. If you can find a receiver that has multiple Sub Preouts, that have independent settings good luck and pull out the $$$$$. The last time I looked, only the top of the line Denon's and a few other had independant multiple sub out jacks and would allow you to set each sub seperately.
I have found that if you calibrate each sub, one by one, then turn them both on you will get good results. Distance (delay) is always fun, especially when one sub has a DSP chip.