You can get a lot of different opinions on this and, in my opinion that's what this is, opinion. I personally use a Sharpie. Sometimes I don't get great hatches, sometimes I get tremendously good hatches. In my opinion the Sharpie is not what makes the difference. I've had three hatches so far this year, 21 chicks out of 28 eggs set, 9 chicks out of 18 eggs set, and 17 chicks out of 19 eggs set. All of them were marked with a Sharpie.
When I was a kid we didn't have Sharpies. Then I used a soft-leaded pencil. A hard-leaded pencil leaves pretty light marks but I'd use the side of that soft-leaded pencil and make some fairly dark lines. They do tend to rub off under a broody hen but the soft-leaded pencil worked. The black Sharpies don't wear off.