Whenever I log into Windows Server via VNC it runs in Console (session ID = 0). Can I change any VNC settings to make it run in another session?
The reason for this is, I want to use remote desktop (rdp) to connect to the running VNC session.
Short answer: no.
Long answer: VNC on Windows typically attaches to the existing console session screen and works its magic by intercepting display changes. The protocol does not have any session tracking capability, it simply provides the crude approximation of a "screen scrape", although it is a very efficient one at that. To do what you want, you would have to get VNC to appear as another viable remote desktop protocol alongside RDP (which is what Citrix ICA apparently does), which implies that Windows would still handle your session; the VNC server would simply provide something to render to.