Question about Rotary setup

I have a rotary i use on 2 differant machines at differant times. One machine i am able to plug into the Z axis and set up is spot on. No problms with the steps per rotation.

The next machine is a CO2 that has no z axis. I have to plug rotary into the X axiz.

When I am not using the rotary, both the X and Y axis are calibrated perfect. Then when I connect the rotary into the X axis the calibration which is the around or across the cups, it is wrong. When I enable the rotary and and adjust the steps per rotation, I am not able to make any adjustments to the engravings.

What can I or should I do so that I do not have to calibrate the axis in the machine settings?
Hope this is understandable.

Edit: Removed leading spaces in paragraphs to prevent triggering Preformatted Text layout. @ednisley

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