Since your using half phase and not single phase it does not matter how you hook the primary, however it does matter which side you put the diode on.
For example, if you pulse high then stop, the diode will pass current on the primary pulse off time.
For example, if you pulse high then stop, the diode will not pass current on the pulse off time, because it passed it on the pulse on time.
The above depends on what side of the secondary you have your diode on, and which way it is blocking.
Do you want the diode to kick on during the Pulsing on time or pulse off time? One way is better than the other since a collapsing field can kick the diode on.
Myself, i just grab some measuring tools to determine which way is best.