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[JAZZCNC]

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.

Even easier way than that if your using the default 1024 screen set. First set the Safe Z in Config (which you really should do for safety reasons regardless) and make sure it works in Work coordinates.
Then all you have to do is type the offset (-2.5 in your case) direct into the X,Y DRO by clicking on each DRO (Must press Enter to apply it) then simply clicking GOTO ZERO button just below DRO's.
You will still need to have the Z axis Zero set equal to the top or above material. The Z axis will retract first to Machine Zero coords because of SAFE Z then move the X,Y axis then return Z axis to Zero work coords.