I have managed to get this to work for the most part.
Enabling dual Y in the advanced settings and then changing all instances of Y2 to E0 has meant that the motors power up etc and when I move Y towards the front of the machine everything works. However, when I try to send Y the other way, the motor that is attached to E0 still tries to go the same way as before I.E. the opposite way to Y?
Can anyone think of what I missed?
I assumed it was a direction in the stepper file but with dual Y being enabled, it looks like all of the directions are already set by Y?