Right now it says:
Paid, Permanent, and Plus S2 accounts: Custom comment pages match your journal's S2 style by default. You can either modify those S2 custom comment pages further or switch to comment pages in your site scheme.
It talks about the site scheme, and about further modifying the customized comments page, but it never specifically explains how/where you can switch between the two (which is usually what I need to tell the user when I look at that FAQ).