Hi,
If you have ACS SE and you want to integrate with MS AD, then you need to install Cisco ACS Remote Agent on a PC that belongs to the domain.
The ACS SE does not "speak" directly to the DCs, but rather to the ACS Remote Agent.
The Remote Agent is the application responsible to exchange data with the DCs.
You can find detailed information in the config guide:
http://www.cisco.com/en/US/docs/net_mgmt/cisco_secure_access_control_server_for_windows/4.2/user/guide/UsrDb.html#wp353636.
HTH,
Tiago
--
If this helps you and/or answers your question please mark the question as "answered" and/or rate it, so other users can easily find it.