What I mean is when you use --webroot, you must also specify the actual root with -w
That "directory" provided with -w must match the directory used in the line root /xxx/yyy/zzz in your port 80 vhost config file (or port 443 vhost config file if the port 80 merely forwards to 443).
That said, I'm now confused by this additional bit of information:
Is the owncloud service running on another server?
Are there more than one server involved in this?
If so, which server does what?