A ground crew accurately measures the survey aircraft's position while the a/c flies a series of manouvres for the aid eg for an ILS something along the lines of:
1. G/s & Loc centred
2. G/s full scale up, Loc full scale left
etc etc etc
I understand the survey a/c has rather more accurate receivers than usual.
Some of the calibration can also involve receivers placed around the navaid transmitter.
Can't remember anymore about it...