how to ftp without overwriting folders but only files (on a mac)

Hi,

Since I switched to mac I still have to find a way to upload files in folder without the ftp tools replacing the folder but just the files.
When doing Upgrades I still use Total Commander from a virtual Windows.

Right now I’m using Transmit at work, Cyberduck at home and I have no clue how to setup those programs to only replace files not folders.

Thx

EDIT: Cyberduck does not replace the folder, only the files. So I got a problem with Transmit.

Forklift from http://binarynights.com/ is my current favorite.