Use WatchDirectory and WatchFTP to automate all your file based tasks.
One thing that bugged my about WatchFTP though was that every time the server was restarted I would have to manually restart the WatchFTP tasks, where as the WatchDirectory tasks could be set to restart automatically. Browsing some of the forum posts I found the answer to this.
Using this I was able to write a start up script to start the WatchFTP tasks automatically.
start "Task1" /MIN "C:\Program Files (x86)\WatchFTP\wfrun.exe" -start Task1
start "Task2" /MIN "C:\Program Files (x86)\WatchFTP\wfrun.exe" -start Task2