It's hard to say what exactly might be going on here, without sitting in front of your machine. My guess would be that you either (1) don't have your remote server selected in the Files window or you have something set up incorrectly in your Site Definition. Usually that's going to be (2) a missing remote root folder in your FTP settings, or (3) a duplicated root folder in your local files.
In DW, click the Expand button (2 square icon on the far right) in the Files window within DW.
Click the Connect button (plug icon)
(1) Make sure you have your Remote Server selected (the bulleted list icon in older versions of DW, selected from a dropdown in CC2017). If it's not and you change it, uploading should work correctly.
If it is selected, you should see the folders on your remote server next to the local site folders and they should be nearly identical. I say nearly because there may be some server files you didn't create, floating in your public-facing server root, things like cgi-bin, error logs, default redirect pages, etc. But mostly, they should be identical.
(2) Your remote server's root folder should be the first line on the server side of the Expanded Files window, something like public_html, www or htdocs (but it could be just about anything, you get that info from your hosting company) and it should be in the same position as your local root folder (whatever you named the site plus the folder path) that you keep the entire site in locally. When you transfer files, you should be transferring only the content of the local root to the server root.
If the server root is missing from your site definition, you'll see all sorts of files on the remote side that you had nothing to do with, and mixed into that list of files will be the server root folder itself. You'll then see the local root folder name, whatever it is, also mixed into that list, which would make the files inaccessible from the internet since they're not within the public-facing server root folder.
To fix this one, go to Site > Manage Sites > click the site > Edit > Servers > click the remote server > Edit > under Root Directory make sure you have the server root entered (if you have nothing, talk to the hosting company and get the info). Once it's added, you should be able to upload and overwrite the correct files with your updated files.
(3) If you've accidentally included the server root folder within your local root folder, everything will be uploading to the wrong location online, but should still be accessible publicly. Try entering your domain name followed by your server root name, something like www.yourdomain.com/public_html. If your site comes up, it would mean you have a redundant root folder that needs to go away.
To repair it, you can move the files from with DW's Files window. Click the +/- icon next to the duplicated root folder in the Files window so its open and showing all files. If a redundant root folder is the problem, it would look something like...
Site - Sitename (C:\path to site folder)
public_html
index.html
page.html
folder
etc...
If you see something like the above, with your server root directory name in place of public_html, highlight all of the files within that redundant root folder and drag them onto the Site - Sitename (C:path to site) line. DW will then update all of your links for you. Delete the redundant root folder and re-upload.
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