Auto FTP Manager has 3 types of profiles - Standard, Automated, and Scheduled.
An automated transfer job can be run manually or it can be scheduled. Manual execution is useful when you do not have a fixed schedule for transferring those sets of files.
To have your automated transfer run automatically, create a schedule for it.
More information on scheduling transfers is available here:
https://www.deskshare.com/help/afm/ScheduledProfiles.aspx