Hi xscott! I just finished doing what you are getting ready to do!
I just found this link on how to make VNC more secure http://www.uk.research.att.com/archive/vnc/sshvnc.html
might be worth a gander. I will be trying it when I get home
I am running into a similar problem with starting the vnc server that you are, my specific problem was that I can start a program when the system starts up, but with RealVNC, the vncserver actually runs based on the user who ran it. So if you run it as Root, your VNC server will be running under Root, etc! So I am still looking for a solution to starting RealVNC at boot time as a different user.
I currently have no linux box with a monitor attached to it, I see no need to. Through my 100meg full duplex connection and RealVNC I feel like I am sitting right in front of it from my Windoze machine! The only things I have enabled on the machine are SSH, and RealVNC. That's all you need!