The target mail store is specified in the migration job when mailbox-enabling. Is it possible to specify different mail stores for different mailboxes?
Export the TSV file for the collection (use the buttons on the bottom right of the Manage User Collections screen to import/export TSVs, not within the Edit collection wizard).
Open the TSV in MS Excel. There is a column called ExchangeMailboxStore, which is blank by default, meaning that the mailboxes will use the default store specified in the migration job. To enable certain mailboxes to be created on different stores, populate this column with the distinguishedName (determine using ADSIEdit) of the required store.
Make sure that the TSV format is retained when saving the file, then import the TSV back into the collection.