I usually use the tip diameter of the cutter as the reference diameter. This can be difficult to measure it it is a 3 flute though. I typically assume that the stated tool diameter (from the catalogue) is exactly correct.
Then, offset the profile of the tapered hole by the radius of the tool at its tip. You can then break or divide up this offset line to create your Z levels. Be sure to check that the horizontal X (or Y) component of the offset equals the radius of the tool tip. If you do a parallel offset by the full amount of the tool radius, chances are that the horizontal component will be too long.
If it is a more complex issue, posting a picture or a dxf of what you have accomplished so far in cadcam would be helpful.