It's begun....

[Jonathan]

Reason for the question is I am zeroing by jogging up to the work piece on each side and setting that axis to zero and wanted to jog by 2.5mm afterwards in x/y to take account of my 5mm end mill,

After zeroing you can go on to MDI, raise the tool up obviously, type G0 X2.5 Y2.5 and zero the axes again. Assuming you zeroed both in the positive direction, the machine is now zeroed. You will probably often want to add a little bit, (G0 X3 Y3) to make sure any cutout pass does make a cut all the way round and not just miss the edge.