One solution is to go mono - that is pick one or the other channel and use it for the sub. There is not much direction in sub level bass, so either side is OK. You could y-split the input if you needed a stereo feed in to your amp.

The side-advantage of this is that you get to choose which phase (==channel) you want. You know that one is x msec off the other, and the sub tuning may benefit from the delay or advance.

Just finished a eq tune in my Mini using white band noise, ear-omerty and fine tune with my favourite music. The cabin is so small and my head is right in a trough between my front 6.5" and my rear 6x9s :| Was hoping I could get front-rear adjustment.