I made a lot of pens this year as holiday gifts. That means drilling holes down the long end of pen blanks. I used both the drill press and the lathe, but settled on the lathe. Here are a few tricks that work for me. I found them by experimentation, so the experts may disagree:
Use a center finder to mark the center of the dowel (or pen blank). I use the center finder from a Starrett combination square set. I tried several different center finders, but the one that comes with the combination square works best for me. It is the V-shaped tool with the blade (ruler) going through the middle of the "V". I make several marks on the wood, not just two. If it is a pen blank, then I make four lines; one for each corner. Sometimes the dowel is not perfectly round or the pen blank is not perfectly square. In that case, the marks may look more like a tic-tac-toe board (hash mark), but the center is obvious. It is better to know if the dowel is not perfectly round.
Use a center punch to create a starter "divot" to guide your drill. I use a Spring Tool because it is easy to aim on the exact center point. I have tried many other center punches over the years, but I like this one:
Use brad point drill bits. I line up the drill bit point exactly on the center punch divot, turn up the rotation speed to fast, and give the drill bit a quick plunge to get the hole started straight. Next, I back out the bit and slow the rotation speed down. Using the starter hole as a guide, I continue drilling slowly, backing out the drill bit frequently to allow the shavings to clear. Don't believe the hype about how well the drill bit clears itself. Even if you see the chips coming out the back of the drill, back it out and clear the chips frequently anyway. I think it helps to keep friction heat down, and gives the drill bit a chance to "breathe" and cool off between cuttings. (Don't brush the chips with an unprotected hand - drill bit flutes can be hot and sharp.)
If you are drilling long holes through thin parts like dowels and pen blanks, then I recommend the special pen making drill bits from Fisch. They are specially designed to drill long straight holes in end grain wood. The problem is that they are only available in the specific sizes that pen makers use:
If you use a drill press, you will need a holder or drill press vise that keeps the dowel or pen blank well clamped, perfectly vertical, and perfectly centered under the drill. If you don't have anything else, try a stacked pair of hand screw clamps at 90 degrees to one another.
I prefer the lathe over the drill press, by far. It does a better job of making long, straight, centered holes compared with the drill press, and is easier for me to set up and use. I use a Nova G3 chuck with the pen jaws to hold the pen blanks or dowels,. I like the pen jaws a lot. They come as a pair, not four jaws. As a result, if you mount the dowel (or pen blank) with a small gap on the chuck side, then it is easy to see visually when the drill has popped out the back of the piece. (Yeah, you can feel it, but the visual confirmation is nice!) The pen jaws are shaped to grip dowels and square/rectangular pen blanks very well. I use a 1/2 inch Jacobs chuck (drill chuck) on the tailstock to hold the drill bit.
The lathe motor rotates the wood in the pen jaws while the operator slowly cranks the tailstock to drive the non-rotating drill bit into the rotating wood. I loosen and back out the tailstock frequently to relieve/release the chips. My friends think I back it out too often, but I think that helps reduce heat and improves the long term durability of the drill bit, and there is no harm to do it.
Jacobs chuck for mounting drill bits on the lathe:
Pen jaws, recommended, both on sale, but the veterans ones are a better price. They fit any Nova chuck:
I have a Nova G3 chuck set, currently on sale. There are also standalone Nova G3 chucks that you can buy, or use a different Nova chuck - any Nova chuck will fit the pen jaws.
(IMPORTANT NOTE: The links above match products that fit my Delta 46-460 lathe and many other common lathes. My lathe has Morse Taper 2 (MT2) tapers at both ends, and a 1 inch x 8 TPI thread on the headstock. Those are the most common sizes, but your lathe may differ. 1.25 in x 8 TPI threads are also common on larger lathes. Morse Taper 1 (MT1) tapers are not common, but I have seen a few over the years.)