There's no interface for setting differential backups - only command line options. In a common scenario let's say you want to setup your full backup to run on Sunday, and differential - every other day. In this case you need to:
1. Create a job with all the settings you need and save it let's say like C:\new.jobx. Don't schedule it in the interface.
2. In Windows Scheduler for Sunday create a task like "C:\Program Files\SQLBackupAndFTP\SQLBackupAndFTP.exe" -r "C:\new.jobx" to do a full backup
3. In Windows Scheduler for Mon-Sat create a task like "C:\Program Files\SQLBackupAndFTP\SQLBackupAndFTP.exe" -r "C:\new.jobx" -diff to do differential backups
Do you need to do transaction log backup? Use "-log" option instead of "-diff"
Do you need to do backup multiple times a day - go ahead do whatever you want in scheduler. Zip files won't be overwritten because they have time in the filename.
Command-line options are in this post:
http://www.sqlbackupandftp.com/forum/yaf_postst25_What-are-SqlBackupAndFTP-commandline-options.aspx