if the directory hasn't shown up yet, then something's going on. Directories created on the server should show up automatically.
I'm not sure how Fireftp works, but I use filezilla and it's basically drag and drop. You'll see files on your hard drive on the left, and the server on the right, and you just drag everything, except for includes, styles, cache_builders/custom from the left to the right and it does the rest.
