If you are using MDT, you can just simply use the below command in the application section. Can't remember of top of my head whether you need to put speech marks anywhere.
FramePkg.exe /install=Agent /forceinstall /Silent
But the MSI way, its is the SiteList.xml that you extracted from the FramePkg.exe. With WDS/MDT you would put this on the distribution share and point the UNC path to there that way you know the permission are set correct.
That did the trick.