I would let Audyssey handle it all. There is no advantage to having it on the subs also. In fact I believe having equalization on both is bad.

The best bang for for the buck for sub equalization is room placement. No amount of equalization on AVR or speakers can compensate for sub-optimal (pun intended) sub placement. Do the sub woofer crawl first and then let Audyssey do it's thing.

For every expert, there is an equal and opposite expert.