Typically, you jog the X and Y axis to where you want the 0,0 position to be, and zero them at that point. You can also use a probe to find the edges, and then set your zero that way.
My machine has fences along X and Y zero, so I just slide the part against the fence, and start cutting.
and with this I am assuming that Mach3, knowing the diameter (6mm end mill) will auto calculate a -3 offset to cater for the tool diameter
No, Mach3 can not auto-calculate the offset. You can program it to use G41 or G42 cutter compensation, but you must prgoram proper lead in and lead out moves for it to work correctly. Most people do the offsets in their CAD or CAM software.