Unfortunately those docs do not help me...  I've already reviewed the docs from Duo themselves including both links you provided, but while the first link shows that you can have 2 different mechanisms for Duo 2FA with ACS, it does not cover HOW to i...

Did you ever get this working?  I'm curious, as I am trying to do a similar setup with TACACS through ACS 5.6 already configured for AD primary authentication and need to enable 2FA with a Duo proxy server.  All the links here, and the Cisco document...