That's a good way of finding the balance point in the saddle (the deepest point). Put the pencil on the rise toward the pommel and let it roll back until it stops on its own. Measure from the middle of your stirrup bar back to that point, then compare that measurement with the length of your foot from the ball of your foot to the back of your boot. If those two are within 0.5" of each other either way, then your saddle will put your leg in the proper position.
But, the pencil trick only tells you if your saddle is balanced front to back. Your saddle could still have other fit issues