You do either way, seal one side or both. I prefer to seal both sides so the hinge line is completely sealed. This will prevent any dirt or debris from building up in the gap between the hinge and the plane.

I explained how to cover hinge gaps in my LT-40 build thread. You can find the descriptions at:
[link]http://www.rcuniverse.com/forum/fb.asp?m=5399213[/link]
and
[link]http://www.rcuniverse.com/forum/fb.asp?m=5589251[/link]

Hope this helps

Ken