Either we know what you want or you can read our minds
We're working on both of these features for the next FlashFXP release. The backups won't be automatic but it will just be a few clicks.
You can create your own automated backups by backing up all of the *.dat files and the flashfxp.ini. Depending on your installation options the *.dat files may not be stored in your FlashFXP folder but rather the Application Data folder.