You can't really tell from this photo, but the best way to paint dots is to use the handle end of various paintbrushes. Just load up some paint and go straight up and down with the brush. I have a few different brushes with different sized handles. I also use a foam brush handle for really big dots and toothpicks for tiny dots.
When I'm finished I plan to give them a coat of varnish to protect them. I have used mainly Martha Stewart acrylic paints because they are thicker than the other brands and so the dots on the sides of the rocks don't slump.
Some time ago I came across Etsy shop owner Elspeth McLean. She paints the most amazing mandala rocks. They are so beautiful. Here is a link to her Facebook Page. I have some more that I am painting and will photograph them when I'm done. Ok back to some embroidery!