It shouldn't be any different, other than you don't have a local video card, nor a local keyboard. This should be a problem, but your configuration is key...
The only thing I can suggest is, however you start X on a normal system (startx), it reads reads the init file and launches the programs in there (usually your window manager).
You should be using VNCServer to since it has its own X server, but it uses ~/.vnc/xstartup first... You should be able to launch the window manager of your choice from that file.
Code:
man vncserver
-Chris