Sounds like a Host Directory issue.
When you connect to your site via FTP, you are probably not in the web folder.
The Host Directory field in the Remote Server category allows you to set the default folder for FTP.
When you connect via FTP, do you see any folders?
If one of them is named 'web' or 'html' or 'www' then that is probably it. You will see your existing site files.
Let's say it's 'www'. You would put that in the Host Directory field. Now when you connect it will go directly to that folder.
Once the Local and Remote sides look the same, you are ready to go.
Hope this helps.
Dreamweaver Quality Engineering