I'm not sure I understand exactly what you're trying to do.. but here is basically the base scenario... Assuming that you want to sit at the vista desktop and want to control the Linux desktop
You would run the server in the linux box. In a terminal, do this as USER... DO NOT USE AS ROOT
If it's your first time running it, it'll ask you for a password... and when you're done w/ the setup, it'll start the server broadcasting display 1.
When that's running, you want to go to the vista box and open vncviewer, in the host field type your linux box's IP address followed by ":1"
it thould then ask you for a password (same password you gave to the server.).