Hi as Aaron points out the RState is the way to do this.
Do know that the MEs are ALWAYS recalled in the RState, think of this like a Memory with it's own Attributes but you are forced to recall all of the elements for the MEs...Only the MiniMEs, MultiScreen, MediaStores and Aux Buses are able to be "ignored".
So Setup of your switcher exactly how you would like to see it after a reboot. Then go to the Memories Tab in DashBoard. Go to the Sub Tab that is RState. Here you will want to enable any of the items that you would like to recall....Aux Buses, MediaStores, MiniME and MS.....remember everything to do with the MEs will be included there are no additional Attributes for them.
Now that you are done -- at the top hit the Save RState Button. Make sure that you Save the File set after this otherwise it will revert the Rstate when you load from USB. This is also a good time to setup the behaviour of the Recall Attributes since this is stored in the RState as well.
#Carbonite