Hi Julian,
1. Any files that are created by default are there for a reason but you may not need them, the _vti named folders are there for compatibility with Frontpage which is a site developing program, if you are not using this you can delete these. The cgi-bin folder is used for storing cgi scripts and this folder should not be deleted even if you are not using it at the moment.
The simplest method for getting files in the public_html folder is to use file manager and just navigate to this folder and upload them, however using FTP software will be quicker and it isn't too hard to figure out, I'd recommend something like FileZilla:
http://filezilla-project.org/download.php?type=client
The www folder isn't actually a folder but simply a shortcut to the public_html folder so it will show the same files, some apps use this path so it makes it easier for them to be compatible.
2. If you provide me the account details via PM that you are using to try this I will have a go myself and see if I can spot an issue.
Regards,
Darryl