stereo subwoofers

Hi,

I am considering buying two Velodyne DD10+ subwoofers to complement my fact 12s.  I gather that they come with a calibration system which allows the subs to "listen" to the main speakes and the room, and then tailor their output to this.

My local dealer said that he would normally calibrate one sub, then attach the second sub and calibrate that one.  My gut feeling is that this would create a setup that is not balanced. 

Has anyone done this kind of setup?  If so, did you calibrate both subs at the same time or one after the other?

Many thanks.