Axis direction help please?

Hi guys, might be a bit of a daft question but just wondering what the typical setup is for homing/axis direction on a moving gantry type router? I ask because mine currently looks like this (left hand rule coordinates?) shown in home position:
Attachment 20479
But most CAM packages seem to use a 'right hand rule' type coordinate system where Y is in the opposite direction:
Attachment 20478Attachment 20480
Have I just got this wrong and simply need to reverse the Y motor in Mach3/home at the bottom right corner of the machine or is there another way of doing this?
Thanks.

You need to use a right hand coordinate system, as that's all that mach3 supports.
The actual Home position can be anywhere you want.

Thanks Gerry, I will reverse the Y axis direction and also reverse the Y home position. This should keep me within positive machine coordinates, as going negative on MC will only confuse me more!!