As far as getting files to your server, if you're in a hosted environment you'll need to figure out what is supported. Typically the file uploads are done via FTP. I'd recommend a solid, robust FTP client like FileZilla, so after a transfer you can confirm that everything transferred successfully. If the files really are extracted on the server already, there may be a file manager available in your hosting control panel. Remember to merge the web.config customizations before deploying the new version.