I never worry about this. As your stock simmers, the joints, muscle and connective tissue break down and eventually they'll sink in. Sometimes adding a bit of vinegar to your stock first helps with this. Until then, just stir the stock and move the bones around occasionally.
I use a drop lid, in a lot of Japanese cooking, the use of a wooden lid which is a smaller diameter than the cooking pot is used to keep foods submerged. But a plate works just a well, it's just hard to fish out of the hot liquid sometimes.