How do we move user's messages into folders?
Retain is an archive so it will keep items where it finds it, often in the Inbox. Retain does not have any file management features so you cannot move items in the user's Retain mailbox.
We do know that it take users a few days to handle their email, but you don't really want to wait to get messages into the archive.
A simple solution is to run a special job over the weekend where the profile is set to go back a certain time period (e.g. 14 days). Retain will update the location of messages that are still on the mail server.
In cases of employee separation is it often a good practice to dredge the employee's mailbox so you have a fresh copy of everything in the proper place.