im having the same issue as Anders,
Basically I have 2 sites for the moment on the same server with an enterprice licens. they are 2 separate sites in IIS but point to the same directory. In web config I have putted down both of them under the <sites><site> tab but now i need to specify another masterpage and aspx page for the other site. I have putted the settings showned in the technical spec of episervers site but nothing happens. i would apreciate some detailed info about it.