Mach3 doesn't think anything, it does what you tell it, your G-code defines the X and Y moves so you need to
change your machine definition in CAM
or
rotate the part 90 degrees in your CAD package
or
swap your axes in Mach3
If you define your zero in CAD/CAM you will know where to set it on your machine, if you're allowing the software to define a default zero you need to note where it is on the stock, you can then set Mach3's zero appropriately,
Regards,
Nick