dgilling,
Per Hondaman's book, I started with truing the wheel by using a straight edge across the rim and getting the hub as close to even on both sides as I could. Measured the distance between the straight edge and the hub with my micrometer.
Then according to Hondaman's book, you need to find the centerline of the bike and mount the rim between the forks. As far as I could tell, the centerline of the bike should be the center distance between the forks. At least that's what it worked out to for me.
Then I simply held the dial gauge against the rim on both sides and checked for axial runout on both sides.
Hope this gives you what you're looking for.
Charlie