If you squirt and swish like most people, allow me to share this better method, which I learned today.  (I learned it by reading the instructions on the back of a bottle of Safety Foam toilet bowl cleaner.)  Before you squirt (and swish), lower the water level in the toilet by plunging it with the toilet brush.  By doing this, you allow the cleaner to better contact stains below the waterline, and keep it from becoming diluted by the excess water.