There is no 3rd horn. By rule, 1st horn is a warning horn, 2nd horn means the time out or intermission has expired. How you handle it is one of the game management decision your crew makes and depends on the specific situation to put the ball back in play.
Resuming play with a throw in. By rule, if it is a delay by the team entitled to the throw in, you put some air in your whistle, place the ball on the floor, and begin your five second count. If they don't get it in before the 5 seconds, it is a throw in violation and you give Team B the next throw in. If team B is delaying, you give the ball to Team A and proceed (most likely with an uncontested layup). If either team continues to delay, it is a technical foul.
If play is resumed by a FT, if the thrower is the one delaying, you place the ball on the line and begin the count. If the defense is the one delaying, you get the ball to the thrower and they attempt their throw. You now have a delayed violation for the defense not occupying the bottom 2 spaces and you have a substitute throw. If they continue to delay, it is a technical foul.
In practice, you don't let them delay. During regular season, we break up the huddle rather than just giving the "1st horn" warning. By break-up, I mean we go to their huddle and stay there until they break. If they delay, we get a coach's attention and make them break. If you need to do it, be sure the crew is consistant and it's better if it is early in the game rather than the last posession.
Mregor