The backup start mat should be placed such that the runners cross it before crossing the main mat when starting the race. The runners can stand on the mats. The runners form up at the starting line as if there were no mats. The timing equipment figures out which of the many signals received from each runner (on the mats) is the actual start time based on the time the gun goes off. This is entered by the timer.
For races with a coincident start- finish line where the runners start and finish in the same direction the mats can be placed with the front edge of the main mat on the start line, the backup mat behind it (runners cross the backup first). After the start the mats must be moved such that the edge of the main mat is on the finish line, the rest of the main mat is past the line. The finish backup mat is placed further past the finish line such that the runners cross it 2nd.