http://en.wikipedia.org/wiki/Inertial_navigationEvery stand at an airport will have the exact lat long position. The crew will put this into the FMS. Using Inertial navigation System (INS (Gyros etc)
) the FMS will know exactly where the aircraft is at anyone time.
VOR's, NDB's and other exact repoting points such as a published Distance on a specific radial from a VOR; will be entered into the FMS along the route.
GPS trials are still on-going, but as far as I am aware it is still controlled by the US. Therefore in theory can be switched off by them.
I am probably out of date, so pilots would be best suited to answer.