Hi,
the voltage output of a transformer is across both output winding connections.
Therefore the usual way is to use method 1)
(with an voltmeter you´d use the same method, too)
Now you are concerned about earth connection.
With a usual transformer this is no problem.
But if the transformer output is related to earth GND already (before connecting the scope) then this may cause a problem.
Then you should use the differential method of 2) and use MATH and show the difference of both channels.
Klaus