That you have all your files in one directory is no problem. It's not a smart thing to do, but it's not a problem.
I don't get your problem.
Do you mean, the transfer doesn't work and the files never get on the server.
Or the fact you can't see you pictures anywhere on the website after you uploaded them to the server?
If it's the first one, and you set up the ftp connection properly, it should work, if it doesn't only the webhost can help you.
If it's the second one, a real website isn't some online photobook. You will need to add the pictures to the site using html. Meaning
![](image.jpg)
should be added where you want the picture.
edit: re-read the question.
If you mean, you can only see the directory if you go to your site's adres (http://site.com). It means you most likely didn't use an index.html. Index.html should be your homepage.