The time should be the total time of the boil with the hops in it.
Most recipes call for a 60 minute hop addition. At that time, I set my timer at 60 minutes and then the clock goes "backwards" to the 20 minute hops (with 20 minutes left in the boil) to the 5 minute hops, and then flame out when the timer hits "0".
So, the 60 minute hops boil for a total of 60 minutes, the 20 minute hops are in the boil for 20 minutes, and so on.
Broken Leg Brewery
Giving beer a leg to stand on since 2006