I don't know much of how TMSXE functions, but my assumption is that any conference that gets created would use the highest priority Conductor alias that is configured in TMS. Of course that would be depending on Conductor is set to be the "Preferred MCU Type in Routing" under Admin Tools > Configuration > Conference Settings. If they'd want to use a different alias of a lower priority, they'd most likely have to use the full scheduler available in the TMS website.
If this doesn't answer your question, or you need more help, suggest you move your post to the TelePresence section of the forums instead of the VOIP section. Can move your post by editing it and changing the categories at the bottom of the page.
