CuteFTP Pro isn't free, but has the best auto-folder synchronization I've seen. It will monitor a folder on your computer and on the server and reflect any changes to either one to the other.
You might also want to give BatchFTP a try -- I reviewed it in the mini-reviews section. It's not free, but it's cheap (15 bucks). It integrates with windows scheduler and can be set to perform scheduled FTP operations in either direction.