David: If it helps any IIRC the previous model, the AVR630, did what you're looking for.
In that receiver's onscreen (OSD) bass management menu, there is an option labeled "global" and "independent". If you set it to global, when you choose "subwoofer-yes", EVERY source will activate the sub output. But if you set it to independent, only that source you *specifically* choose to have "subwoofer-yes" will activate the sub output (I
think the source to be configured is the one that was chosen immediately before the OSD was activated, but am not sure about this).
In other words: choose the CD input first, then pull up the b.m. OSD, choose "independent", then choose "subwoofer-no". I think that should do the trick; otherwise I would email/call Harmon themselves.
We rarely messed with the 630's b.m. system during those six months, since we always ran all speakers large

+ subwoofer-yes.