Why bother to scribe a centerline at all (and, yes, you shouldn't use a center drill as a scribe)? Once you've located to the (unscribed) center line, zero your DRO and take all further measurements as offsets from that datum.
When you get around to doing bolt circles by coordinates, have a look at the BOLTCIRC program on my webpage. It will calculate all the coordinates you need for the holes automatically. Here's a sample of the output it generates for a five hole circle:
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Boltcircle specification:
Radius of bolt circle = 3.0000
Bolt hole diameter = 0.5000
Spacing between hole edges = 3.0267
Angular offset of first hole = 0.0000 deg
X offset of bolt circle center = 0.0000
Y offset of bolt circle center = 0.0000
HOLE ANGLE X-COORD Y-COORD
1 0.0000 3.0000 0.0000
2 72.0000 0.9271 2.8532
3 144.0000 -2.4271 1.7634
4 216.0000 -2.4271 -1.7634
5 288.0000 0.9271 -2.8532
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If you don't yet have a rotary table, this program can help a lot. (Many of Elmer's engines call for bolt circles on the cylinder ends.) Even if you do have a RT, the program will save you the hassle of swapping the vise out, mounting the RT, then reinstalling and rezeroing the vise just to make one small part.
You want your edge finder spinning because what you're interested in is the spin axis of the spindle, which may not be coincident with the mechanical axis of whatever is grasping the edge finder. Using the edge finder in the drill chuck is acceptable, but you really do need to have it spinning.
Observe the edge finder from a direction orthogonal to the direction in which you're moving the table. You'll be able to pick up even a slight offset more easily.
Not all edge finders are made equally. A good one will snap off a considerable amount as soon as it goes slightly over center. Poor ones may be sloppy and displace only a very small amount.