I have a series of 3/8" dowels cut to 4" in length, then sharpened in a pencil sharpener capable of sharpening the larger carpenter's pencils. Some dowels are about 1/16" at the point and they increase slightly in size until they reach about 1/4" which get used on larger flathead jigs. The 1/16" tip does the first color, then I use a blunted toothpick to do the second color. Just barely dip the sticks in the paint and just barely touch the top to the jig, then repeat for the other side. When all jigs have the base color, clean the stick and go to the next smaller stick to lay on the second color in the same way as the first.
I use the vinyl jighead finish available at many shops and stores, online and right here at Do IT. I thin the paint to get rid of "stringing" when the paint is first used. If a head is dark, the first color will be white. If the head color is light, I use black first.