Long before there were stick on eyes, I used drill bits, wooden dowels and a pencil sharpener to make a double ended tool for two colored eyes, Sharpie markers work for some applications.
Depending on jig size, "tulip beads in a bottle" paint makes some interesting eyes
Also, you can try a thin layer of your color on a flat surface then tap the jig one time and turn it over and tap the second side. Do not tap in same spot twice, Depending on paint layer thickness you can make small to large eyes. Plus a little goes a long way.