You would need to add your files as a "website" if you're using the x10 Basic cPanel theme. A "website" in that theme is about the same thing as a "project" in some other software - you can have all of the files you need, but they haven't been grouped together and given a name yet. Or you can switch to the x10 x3 theme instead, which doesn't use the "website" idea and just use ordinary file management.
I don't have access to the back end of your site, so I can't be of much help with the zero-byte issue, but that's often because you've reached your quota. again, I can't say that's the case here, but it's something to check.