There are two different forms of delete in Multiload which may be the source of confusion.
Multiload Delete Task accepts a DELETE statement with a where clause intended to bulk delete the rows qualified by the where clause. It does not import any data so does not have a work table like other Multiload operations. The advantage of using this over a normal SQL Delete Where is that it is not journalled but is restartable (can't be rolled back but can be finished).
Multiload also has a delete where a list of keys is provided from an external source to identify specific rows to delete. This form imports the list of keys to a work table, then performs the delete during the apply phase. The work table in this case contains just the imported keys.
The same way any data is loaded. A souce is decribed that contains the PI values to delete and multiload is told to load those PIs and then use them to delete rows.