The credentials that you specify in the grid synch settings are for connecting to the target domain during the sync to retrieve the list of computers to be synchronized. Currently that is their only purpose/function. We will consider your desire for a future version. In the meantime the way to accomplish your goal is to put each separate domain in its own BatchPatch grid, and then use the grid’s row template feature to automatically populate the alternate credentials fields in the grid when hosts are added during a synch.
Row Template Configurator