They usually show the more popular Fathom Events on the bigger screen. Also apparently in June there is a Judy Garland's 100th birthday celebration event and during the ad for it they only show clips from the Wizard Of Oz so I have no idea what that event will be.
Just looked it up, apparently...
I went to today's Fathom Event there were maybe 10 people there which was made worse because they put it in the auditorium with the biggest scope screen and what I think has a seating capacity greater than the IMAX theater on the premises. They showed a featurette on redoing the visual effects...