It depends on the size of your tonsils and how inflamed they are. The stones form in little pits in your tonsils called "creeps" and every tonsil has different creeps in different areas. Some are far back and hard to reach, some are right there on the surface.

The method that works for me is to take my toothbrush (make sure it is bacteria free) and while closing the glottis in a strong "swallowing" fashion, you help protrude the tonsils out more. You then use the toothbrush to simultaenously move the soft palate out of the way while pushing on the tonsil in a sideways fashion. Gently explore different angles and depths and see if you can find the creeps and even expose some stones. Sometimes it is easier with a dry toothbrush because of the added friction, sometimes it helps with a lubricated toothbrush like in the middle of brushing you teeth.

Tonsil stones are the real cause of the "bad breath" smell and keeping your tonsils free of stones will give you truly fresh breath, provided you are eating right and hydrated.