Download Last build of APBackup. In the new bild new option was added. You can select kind of backup (Full or Incremental).
In old version you should go this way:
In this case you should set "Include only if archive attribute is set" and "Clear archive attribute".
But if you want to organize incremental backup there is a way:
First you should create one task for starting one time per week (for example) for full backup and set only "clear archive attibute"
After you should create second task for everyday start. In this task set both of flags and depth = 7 day. So, second task wil be create only incrementel copy every day and you have full backup+ last few days changes backup.