This is not possible by design. But with some tricks you can achieve the same result:
 
- Go to the Settings->Queue
  and enable Start Queue on startup
- Queue all the files you want to transfer into the global queue.
- Save the queue file
- Make the queue file read only
- Add the SmartFTP.exe to the windows sheduler.
 
I hope this solves your problem. An internal sheduler is planned for the next release.