From what I understand (from being a team owner, not running the actual league), is that the program does everything for you, as long as you input the information. Basically, it makes everything so much easier, and keeps track of everything.
You can adjust depth charts (the person(s) running it have to edit those in the program), edit players, etc.
Then, when it's time to simulate the games, the program gives you the box scores, and all the statistics, standings, etc.
It's a great program, from my short experience playing in a league that uses it.