|So you are using RemoteApp services and you want to deploy the msi you create for the RemoteApp to the user?|
Do I follow you correctly?
If so, you can create the MSI within RemoteApp manager, then publish that msi via group policy like you publish any other msi.
When creating the msi in RemoteApp manager, you can define that you want the shortcut on the desktop of the client machine.
Hope that helps.