You can use the plugin command once at the start of your game, so it could be in the intro scene of your game. You don't need to run it again every time a saved game is loaded.
This plugin command is there because some fights you may want to hard code a certain BGM for, such as a boss battle, so it lets you turn the plugin ON/OFF mid-game as needed.
For example, you might Set Control to true at the start of your game, then to false right before a boss battle that you want specific music to always play, then back to true right after the boss battle.