Jamie
The hole doesn't have to be centered exactly. There are only two requirements - first, that there is enough wood all around the hole to be able to turn the pen body, and second, the hole must be straight which means that the blank cannot shift while you are drilling.
Here's how I do it. I start by finding the center of the blank either by drawing corner to corner lines on the ends, or by the more approximate approach of scribing lines on the ends that are parallel to the edges of the blank to create a small square (or rectangle), and then eyeballing the center of the rectangle. I use an awl to create a small dimple at the marked end points.
The next step depends on whether the blank is approximately square in cross section. If it is square, I simply mount it in my scroll chuck using pin jaws. using the tailstock centered on the dimple to align the blank. Tighten the chuck jaws, and drill.
If the blank isn't square, I mount it between centers and turn a tenon at one end that I can use to mount the blank in my scroll chuck. Align as above, and drill.
I usually start drilling with a center bit just because I have one and I'm fussy. That step isn't really necessary if you are using a brad-point bit - just center the brad point in the center dimple and drill.