You will need to create a new automated transfer profile which will allow you to select and schedule your FTP transfers. To create a scheduled transfer, select File ] New Profile ] Automated Transfer Profile. Next, you will need to fill in all your FTP information. On the Transfer Tab you will see a filter option. You can set the filters to transfer files that have been modified today or within a given date range. You will also see a schedule option where you can set the time and dates to run this profile.

For more information on filters you can see the following article:
http://www.deskshare.com/resources/articles/afm_AdvancedFiltering.aspx