My AutoArchive seems to have been working OK, but when I check I found out
that it seems to be backing up the Sent items but not the incoming mail
folders.
Archiving is NOT, NOT backing up. Archiving and backing up are completely
different operations.
Autoarchive moves items from your main data store to a second PST based on the
date criteria you set, comparing that date to the modified date of the items
in your data store and moving those whose modified dates are older. A backup
is a _copy_ if all the data in your data store.
Perhaps the reason the items you think should be archived are not being
archived is that their modified dates are newer than your archive time
setting. Perhaps, also, you've set those folders to not be included in the
archive process. You should check those things.