My apologies, I entirely seem to have misinterpreted your question, which still looks like what I thought it was to me LOL. I guess in the end you're still just right back where you started at not really having this uploading correctly the way it sounds to me. In the program you specify what directory you are planning to put the shop in by just filling in the path for that directory. In my case all that's in that box is the words /public_html/shop/. If you put the correct location in that spot, then upload to exactly that location which would be:
root or havelock.net's public_html area /boatstuff/ shopnamehere
You HAVE to upload it to exactly the same place that you have stated in the Program for the Remote Folder or you won't have things where you think they are.
From what I'm seeing when I go to your link, you're trying to put it into a subdirectory of the havelock.net site called boatstuff. So what you need to do is inside the SCC go to the area that you put the server details in and type:
/public_html/boatstuff/shopnamehere
Then when you export it to upload it manually (which is what I'm assuming you're doing) you upload all the files into the /public_html/boatstuff/shopnamehere location of your server.
It's that simple, just that the 2 places need to coincide for them to work together. Basically goes along with the "you must have the same site structure online and offline for you to view your content items correctly in the html editors" type thing. Just that we don't get to see what that structure actually is with the shopping cart, you just have to trust that whatever you put into the server setup's remote folder is what you need to do on the server side.