In Cut2D, you pick an origin, which can be lower left, lower right, upper left, upper right, and center. Typically, you'll want to use lower left.
In Mach3, jog your machine to the lower left corner where you want your part to be, and zero the X and Y axis. Then run your code. You'll also want to zero the Z axis to the top of the part. Make sure that's how Cut2D is configured as well.