Best way to approach a referee

[dkmz17]

How do you "handle" a referee that misapplies a rule etc., during a game, especially if it is a circumstance that will repeat during the game.

Recently, I was involved in a summer league game with 9th and 10th grade girls. The rules for the games are NFHS rules, except that the clock only stops on time outs until the last 2 minutes of each half, at which time the timing is handled as per NFHS rules. Also, the summer league rules specifically state that after a time out by the coaches or an official time out, the clock will restart as it normally would after a dead ball.

Near the end of the second half, with 3:30 remaing in the game, we were called for a foul, sending the other team to the line. Since under the summer rules the clock would continue to run during the free throws, I called timeout to perserve the time on the clock. However, after the time out ended and and the teams lined up for the free throws, the referee told the clock operator to start the clock as soon as he gave the ball to the shooter. I complained that the clock should not start until a throw in after made free throws or until it was touched by a player or touched the court after a miss. The referee told me that the ball became live and the clock started when he handed the ball to the shooter. When I complained again, he told me I needed to "read the rules" and insisted that the clock run.

What can or should be done by a coach in that circumstance?