@mattyd to set X0 Y0 to set the bottom left and positive movement to be correct you should do the following:
Set the motor directions using the M569 commands in config.g (or in your case, probably in config-drives.g) so that positive X is to the right and positive Y is away from you. Change the M574 commands to set the endstops to low-end (e.g. X1) instead of high end (e.g. X2). Change your homing files to move in the negative direction instead of the positive direction.See https://docs.duet3d.com/en/User_manual/Machine_configuration/Configuration_cartesian. I am assuming that your machine is Cartesian, not CoreXY.