Not at all my area of expertise so someone smarter than me may jump in and correct me here . . .
My understanding is that you make a QSUB election for the subsidiary S Corps and doing so effectively turns those S Corps into disregarded entities for tax purposes. You would consolidate the books outside of the tax return process (i.e. Excel) and just report the totals on the "consolidated" S Corp return. But since it's just one entity for tax purposes, there's no need for a consolidated check box.
I'm not sure how you'd get to S Corp w/QSUBs from C Corps owning C Corps so I have no idea where those land mines are buried. Tread carefully. 🙂