You might need to run the set up one time for each separate sub if that's the case.
users should try separate & together. My concern for users is the EQ for one sub may complement or clash w/the other.
For that matter, EQing one channel or sub at a time doesn't allow the software to adjust the channel's output particularly in the lower octaves. You may end up w/a "bassy" sounding system and not understand why.