If you are not running Ability FTP Server as an NT Service then this is very simple. It can be achieved by specifying the shared folder in the same place where you would normally specify a local directory path. However, the shared folder cannot be accessed via a mapped drive and so you must use the full path name (e.g. \\pc1\shared).
If you are running the software as an NT Service then the procedure is the same as above but with an additional step. By default an NT Service runs under a default account which has no access permissions to shared folders on other computers. To gain this permission you will need to change the account which the NT Service runs under. This can be done by entering the Administration Tools and then opening the Services option dialog. Once opened, you can adjust the properties of the 'Ability FTP Server' service and set a different account. For the changes to take effect you must restart the Ability FTP Server NT Service. Please note that the only problem with changing the account is that you will no longer have the system tray icon for Ability FTP Server when running the NT Service.