You can choose to accentuate your holes with a bead, especially the primary holes. I suggest experimenting to see what you like, or just mix it up.
You can cut beads with whatever tool works for you. I suggest using a 1/8" beading tool on the primary holes. Sorby makes a 1/8" tool that's easy to use. Be sure to cut in with the beading tool toward the center of the ball so the bead looks right.