I use a 1/4" dowel stick that's been sharpened slightly in a common pencil sharpener. The end of the dowel used for the smaller dots is about 1/8" and the larger dots come from using another dowel with a tip diameter of about 3/16". I open the mold and determine which half is the top. Then I heat up plain black scrap plastic until it can be stirred some, add a shot of stabilizer and then jack the temp up to about 360 degrees. I use the dowels by dipping the end in the plastic just far enough to get it to stay on the dowel and then quickly tap the dab of plastic in the mold where I want it. This is repeated for each dot and where a different size dot is wanted a different sized dowel is used.
I've mentioned this before....6" bamboo skewers and tooth picks are the handiest tools one can have around the shooting bench, these closely followed by a teaspoon and the dowels just described.