Except for the last 2 minutes of the first half and the last 5 minutes of the second half, when a ballcarrier goes out of bounds the clock is only stopped until the ball is made ready for play and then it restarts. In the last 2 mins of first/5 mins of second we go back to the rules God intended and the clock stays stopped until this snap.
(This was a timing change in the 1990s because "they" were complaining that games were taking too long. So instead of giving us less commercials, we got less football.)