The way it was explained to me was this...
When there's a play on the batter-runner, the batter-runner must use the colored portion of the base (with the exception that you mentioned of a throw from foul territory).
Once that play is over, the double base essentially becomes one base. The offense and the defense are then able to use either portion of the double base.
Sounds like you made the right call, but for the wrong reason (at the time that you explained it to the coach).
