Matthew's method would probably prove to be the most accurate, since you don't have to worry whether your logic stutters if the computer lags. al_get_time() will return the current time now, regardless of the speed of the processor.
That being said, you may also want to create a custom timer that includes the ability to pause. You don't have to use the pause feature, but you don't have to reinvent any wheels as soon as you decide that you would like one. Just tell whichever time you're using to pause itself while the game is showing the menu, and then unpause itself when the game "resumes".