You would create a custom document type that would simply be a place holder for your transformations. Do this in the CMSSiteManager by creating a new document type and selecting "The document type is only a container without custom fields".

Your transformations in that new document type will need to have the field names in them based on the data source utilizing the transformation. For instance if your one data source has 3 columns (FirstName, LastName, UserName) you use those in one transformation. If your second data source has 4 columns (EventID, EventName, EventLocation, EventDate) you can use those in another transformation but they would both reside in that custom document type you created. You'd then assign the transformation code name to the repeater and you should have your data displayed!