First, you have to place defrag.def in the right directory. This file contains all defrag entities definitions (target_startTimer, target_stopTimer, target_checkpoint and many other stuff). So if you use Q3radiant, you have to put it in tools dir (for example: C:\Program Files\Quake III Arena\Tools\defrag.def), but if you use GTKradiant, you have to put it in scripts dir (for example: C:\Program Files\Quake III Arena\baseq3\scripts\defrag.def).

Start the timer: Create a trigger_multiple over the area you want your timer to start (over the start line and up to the roof usually) and point this to a target_starttimer.

Stop the timer: Create a trigger_multiple over the area you want your timer to stop (over the finish line and up to the roof usually) and point this to a target_stoptimer.

Checkpoints: If your map is long and/or has different sections you can put checkpoints in the map by creating a trigger_multiple in a doorway or around a teleporter (or anywhere you see fit) and pointing these to a target_checkpoint entity. Notice that checkpoints will not work if cheats are on.

Since the hobby of many bad players is to find a way to reset the timer after collecting all weapons and powerups in the map, you have to place it right. The best clue, i think, is to make a spawn room with only a teleporter who will teleport you to your second room, of course the timer trigger has to be inside the teleport trigger.

Thanks to Gambit