Installation of MS patches should not be necessary on the appliance, nor is it supported. The Windows used on the appliance is a very cut-down version, has a packet filter installed also, and only the very necessary ports are opened up on it.
Patches for ACS will be released every now and then when a problem is found, but not just for any standard MS security bulletin since most of them don't apply to ACS and the version of Windows running on it.
Having said that, the first version of ACS Appliance was susceptible to certain viruses, the Welchia worm for one, and a patch was released for that. Since then we haven't seen any patched appliance get infected.
Patches for ACS are kept here:
http://www.cisco.com/cgi-bin/tablebuild.pl/solution_engine
Read the readme files associated with them to see how to upgrade.