Adding hops early in the boil releases and isomerizes alpha acids, which makes the beer bitter. Since they have been boiled so long, they have very little flavor or aroma. Later in the boil, the acids cannot isomerize, so they don't impart bitterness, only flavor. At the end of the boil, the acids aren't release, only aroma. That's my understanding anyway.
The directions should have told you which was used for what. If so, add bittering when you begin the boil with 60 min remaining, flavor with 20 min remaining, and aroma at flameout or a minute before.