It sounds like you have almost got it worked out, you may want to try a couple of different variations on this to see if you can get it to work. You should try setting the upload folder to be
leaving off the beginning slash so that it does not try to start at the root of the site. If you continue to have problems with this please let us know and we can help you try to get this resolved.
As for uploading the folder and it's contents all of the time this is not necessary, the files should stay the same for the most part, you should only upload them again if you see some results that do not match the current configuration that you have or if you encounter any errors related to pages not being found.