I'm not sure what you want. $game_variables[1] = 15 (with an extra s) does in fact set the first game variable to 15, so if you just want to set a game variable with a script, it's all you need to use. $game_variables[1] == 15 on the other hand is used to test if that variable is equal to 15, which is like using a conditional branch where a variable is tested to be 'Equal to' some constant number.
If that doesn't answer your question, please elaborate on what you're trying to do.