SFTP setup between two sites between windows and AIX server

I have Server ruing Windows 2008 with SFTP service in site A. I have another site B having an AIX server with Network storage attached and SFTP service enabled.

Couple of questions:

1. How can I transfer only the folder structure without its contents from windows server in site A to site B server ruing AIX server? I do not want to use "-r" option which copies folder contents also.
2. Using EDI , I need to transfer the folders and files as a batch process as and when a new file/folder is added. How can I automate this?

Thanks for your help.