I have done this by cutting off a round wooden toothpick about 1/4 of the way along the shaft to make a flat round end. Dip the flattened tip just barely in a bottle of Testor's model paint (because that's what I have) and place a dot where you want it. The toothpick should hold just the right amount of paint to make a small dot about 1/16 inch. I have found it easiest to align the dots properly by assembling the rod with the best visual alignment that I can manage and then placing the dots either side of the ferrules so that they line up.

Hope this helps,
Ted