I use acrylic craft paint and a culture swab. I let the first coat dry and then check for light transmission. If I shine a flashlight on the outside of the blank and see obvious light spots, I do a second coat and the let dry overnight.
I do not generally paint the tubes, but if I am really concerned about show though then I use a brush type Sharpie to color the tube and will even mix a little of the acrylic paint into the epoxy to color it, it only takes a drop or two.
I like the culture swabs, which are long wood handled one ended q-tips because of the length and that they are less fuzzy so they don't leave cotton fibers in the paint.