seperate?
IIRC, the equalizer always was a separate box from the speakers.
Yes, you do need to use it with those speakers. They alte rthe signal sent to the speakers so the bose speaker doesn't sound like total sh!t.
Insert it between the preamp out and the main amp in for the channels that the Bose speakers are on.
I'm both surprised and disappointed at the answer you got from Emotiva. They obviously aren't familiar with those speakers.