Are you sure that your uploaded theme file was not too big for server to handle? For me your theme is showing up fine, which index files exactly disapperead?
I suppose you want all your 6 subdomains to have that theme? Then you just upload the theme to your sub directory htdocs folders. Find folder on your File Manager that is http://name-of-your-subdomain.sub.com and then find children folder called htdocs and you can simply upload your theme files to the htdocs folders of each subdomain.
Is this what you are trying to do?
If i misunderstood you or you are having other kind of trouble do not be afraid to ask for help again.