How do you determine the phasing of the windings of the secondaries?
This
only matters if you need to connect 2 or more different windings in parallel or series. If each is being used on its own (as is typical in most guitar amps), then phasing of windings is irrelevant.
... He says to connect two secondary windings in series and then measure them. How do you connect them in series? ...
Pick a winding. Call one lead "#1" and the other "#2". Do the same for another winding. Apply power to the primary and measure the voltage present on each winding by itself. Take one winding's #2 lead and connect it to another winding's "1 lead. Apply power to the primary and measure voltage between the two remaining leads not connected to anything. If the voltage is the sum of the individual winding voltages, then lead #1 of each winding will be the same phase; if the voltage is the difference of the two windings, then lead #1 of one winding is in-phase with lead #2 of the other winding.
What I described was placing the windings in series, and you'll see it's just like any other component type being placed in series.
So for instance on my Marshall 50w if i wanted to determine secondary phasing how would i do it with the PT obviously connected in the amp? ...
This doesn't apply to your 50w Marshall because you're not attaching any 2 windings to the same point/component. Phasing
only matters when you connect one winding directly to another, either in series or parallel.