REW with subwoofers

I’ve searched this topic but have yet to find it specifically addressed online.  I’m getting ready to run REW for the first time, but am uncertain whether or not I should have all my subs on for the measurements.  I have multiple subs connected high level underpinning my bed layer speakers.  I also have dual subs connected to my LFE out.  I ran YPAO without the  high level subs connected and subsequently dialed them in to the YPAO-corrected system.  My next step is to run REW for every speaker and my LFE subs.  To me, it now makes sense to have my high level subs connected for my speaker measurements, but I’m not sure.  I’m hoping someone here has experience with this.

Thanks. 
Pat