Cyberduck is the least confusing interface and I love using it, but if you need to do detailed file work (many files or a lot of arrangement) transmit is the better option because it gives you a split screen dual browser which allows drag and drop from your mac to your phone without having to go hunt the file down on your mac and drag it all the way back to the spot you want to drop it in cyberduck.
Once you use it you'll only open the ducky for quick tasks.
On the left is your mac file system, on the right is your iphone file system. you can navigate either one and drag/drop to the other back and forth flawlessly. You'll also notice the spotlight search bar in the top right to SEARCH the iphone file system. Overall a helluva program.
http://www.panic.com/transmit/