I'm new to running ACBF and I know there are cutscenes you can skip by quitting the game but I need to all the cutscenes you can skip and when you quit the game and then rejoin the game to skip cutscenes, do you need stop the timer once you leave the game then resume it when you rejoin the game or do you let the timer run while you are leaving and rejoining the game?

You let the timer keep running. Timers do not pause during RTA runs