I take it you're using the EIA software...
Just simply tell the machine where its touching in the code like this:
G65P9811Z.390S111 (Tells the machine Z0 is .39 from the surface touched)
For Y
G65P9811Y-.1815S111 (Tells the machine Y0 is .1815 from the surface touched)
Etc, etc.... The P call would be whatever sub number your macro uses. Most of my Mazaks happen to be 9811 for single touch surface.
EDIT:
In your case, since you want to tell the machine zero is somewhere else because you're setting from the fixture, you can do this....
G65P9811Z-.390S111 (Tells the machine surface touched is -.390 from 0)
and
G65P9811Y.1815S111 (Tells the machine surface touched is +.1815 from 0)
HTH
It's just a part..... cutter still goes round and round....