It is possible to install Microsoft System Center 2012 Virtual Machine Manager (VMM 2012) and App Controller on the same computer, although as a best practice and for better performance we recommend that you install these server roles on separate computers.
However, if you must install both server roles on the same computer, we recommend that you use one of the following methods…
For all the details please see the following:
KB2933853 - Information about installing Virtual Machine Manager and App Controller on same computer (http://support.microsoft.com/kb/2933853)
J.C. Hornbeck | Solution Asset PM | Microsoft GBS Management and Security Division
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System Center All Up: http://blogs.technet.com/b/systemcenter/ System Center – Configuration Manager Support Team blog: http://blogs.technet.com/configurationmgr/ System Center – Data Protection Manager Team blog: http://blogs.technet.com/dpm/ System Center – Orchestrator Support Team blog: http://blogs.technet.com/b/orchestrator/ System Center – Operations Manager Team blog: http://blogs.technet.com/momteam/ System Center – Service Manager Team blog: http://blogs.technet.com/b/servicemanager System Center – Virtual Machine Manager Team blog: http://blogs.technet.com/scvmm
Windows Intune: http://blogs.technet.com/b/windowsintune/ WSUS Support Team blog: http://blogs.technet.com/sus/ The AD RMS blog: http://blogs.technet.com/b/rmssupp/
The Forefront Endpoint Protection blog : http://blogs.technet.com/b/clientsecurity/ The Forefront Identity Manager blog : http://blogs.msdn.com/b/ms-identity-support/ The Forefront TMG blog: http://blogs.technet.com/b/isablog/ The Forefront UAG blog: http://blogs.technet.com/b/edgeaccessblog/
Another way to get around this is to assign multiple IP addresses to your VMM/App Controller Server, create a DNS record for the new static IP then bind that IP and DNS name to the AppController web app with a valid Cert. VMM only overwrites the '*' Binding for 443, not specific IPs using 443.