App-V Sequencer creates applications that can be run in a virtual environment. It monitors the installation and setup process for an application, and it records the information necessary for the application to run in a virtual environment.These applications does not interact with OS as they runs in virtual environment.
You can deploy the sequenced applications using SCCM 2012 to User based computers in more suitable way using Global conditions.
Somaning has shared his experience in sequencing SCCM Configmgr 2012 Admin Console using App-V 4.6 SP1 tool for Windows 7 64-Bit Service Pack 1.
For best practices how to sequence an application : http://technet.microsoft.com/en-us/library/dd351420.aspx
would like to know how to Sequence SCCM 2007 R3 admin console ,Please refer http://blogs.technet.com/b/appv/archive/2012/03/20/how-to-sequence-the-system-center-configuration-manager-2007-r3-admin-console-with-microsoft-app-v.aspx
Note:If you are deploying the sequenced applications to clients using sccm 2012,ensure you have the Right version of App-V client on Target computers.The Supported version is App-V 4.6 SP1 cu5 !
If you are running issues like app-v service receives an exception and then crashes ,the service cannot be started because of the lost of the file system,You may have to install the hotfix available here on http://support.microsoft.com/kb/2693779