Please see our wiki page on programming, for the “getting started” guide:  http://wiki.evilmadscientist.com/Art_Controller_Firmware
Look for this part of the code, where the trigger is issued:
                    if (PINB & 1)  // Make sure that cancel pin is HIGH (not active):
                    {
                        resetTimer();
                        StopTime = calculateStopTime();
                        TurnCoilOn();
                        Triggered = 1;
                        CoilOn = 1; 
                    }  
 
What you will want to do is to add the three-second delay at this point, maybe like so:
                    if (PINB & 1)  // Make sure that cancel pin is HIGH (not active):
                    {
                        resetTimer();
			StopTime = 3;
			while ( seconds() < StopTime)
				{}
                        resetTimer();
                        StopTime = calculateStopTime();
                        TurnCoilOn();
                        Triggered = 1;
                        CoilOn = 1; 
                    } 
 
(Keep in mind that this is untested code, but it might point you in the right direction.)