There are two key questions right off the top. Are you having problem loading your user site virtual host (ie: /) properly <i>or</i> with the urls eZ publish generates being not quite correct?
You might like to take a look at this thread which talks about these issues and requirements a bit.
It might also help us to more quickly trouble shoot your situation if we knew your full apache vhost / .htaccess configuration, override/site.ini.append.php and that your using ezroot (url) operator in your templates instead of ezurl.
