Focus Spread for Macro Photography

I was hoping that the experienced macro photographers could give me a hand here. I just picked up a Nikon 120mm macro lens and have calibrated my monorail for exposure compensation as a function of bellows draw. So far so good. Now for focus spread. In order to ensure I'm covered for the very limited DOF available, do I use the effective aperture (i.e. lens aperture x magnification), or do I consider only the lens aperture as I would for any other focal length?

Effective aperature, which is why diffraction becomes an issue in a hurry.

Cheers Ed. I was afraid that the was the answer.