Observing the behavior of plasma around the Sun is probably one of the indicators. Also, the Zeeman effect in the Sun's spectrum measures the absolute intensity quite directly; I'd assume that the zero transition could be observable this way.
Once they observe the photospheric magnetic field, they use it as a boundary condition for models that project upward into the corona. They can't observe the field directly in the corona (this might be an experimental capability somewhere, but it is not done observationally anywhere).
They do observe the movement of plasma in the corona, to check the field lines predicted by the models.
