I agree with Isaiah - I think the site is missing some bits. I have quite a few S3 sites up with MapSnaps embedded - and all of them look great. You can see an example here.
Due to company policy, I have to edit the source code of my sites before uploading them to the server- so I pretty much do what you do (although I use Fetch). To keep things simple, I create a folder called “docs” at the root of each of my sites. Into this goes all of my warehoused items (images, movies, PDFs, etc). It makes it a breeze to upload new files, as well as to keep a full archive of my last good upload. To make things stand out even more, I use the color tags built into Finder - for example, any folder that never gets deleted is red (docs, MachForm, asp_client, etc.), orange is restricted via robots.txt (last good site goes in here), and green are generated by RW.