They're used in a straight up-and-down stipling motion, rather than a long swoop side to side or up and down.
The main advantage of a stencil brush over a normal paintbrush is that it reduces the chances of getting paint under the edge of the stencil because of the stiff bristles.
Don't overload the brush with paint. Dab just the end of the bristles (the hairs) into the color you require. Having only a little paint on the brush means you have more control over it. It's better to dip the brush into the paint frequently, as it's far easier to add a little more paint to a stencil you're painting than it is to remove it, without creating a mess.