Have you used older versions of PC-DMIS that used the Xact Dimensioning? I believe you used to be able to edit the Nominals from that window, but is no longer possible with the new Geotol Dimensioning method. As Neil said above, you'll have to modify the feature's theoretical values.
+1 on what Neil said. When programming from CAD you may need to "lie" in the THEO so when you tolerance the feature is shows what the print does. Design people don't know the aggravations that they cause by rounding up or down. In the medical OEM world they cause me a lot headaches by doing this.