[dnanian]

You'd partition the backup into two volumes, one for each source. Depending on how you're telling the system where the files are, you'd name the user volume the same as the source (eg "User Drive" or whatever), then schedule two Smart Updates.

Note that I'd probably create one account that had its home folder on the SSD, too, in case you need to do some things when the user volume was messed up or made incorrectly.