Remote copy folder

I have a large folder on my webserver which I want to backup to another folder on the same server.

Is it possible to generate the necessary commands with smartftp (and execute them)
or is this beyond the scope of smartftp ?

The first requirement is that your server supports FXP. If this is the case you can create a FXP transfer and add it to the Transfer Queue. See the howtos for FXP transfers at:
Once you have queued the transfer in the Transfer Queue you can schedule it and run it multiple times. For this right-click on the item in the Transfer Queue and select "Schedule" from the context menu. This is what can be done in the SmartFTP Client application itself. If you need to customize the process further you might want to look at the SmartFTP FTP Library component.