The depth chart allows you to indicate how much action a certain player gets. The SimEngine uses your depth chart to determine who gets on the field for each play. Players at the top of the chart will get into the game in an attempt to get reach their expected number of touches. Players will go out of the game if they are being used more than their Stamina allows or are becoming fatigued from playing. Players lower in the depth chart will come in when the higher depth guys need to come out.
Quarterbacks will typically play the entire game unless they are being overused, and if they do need to come out of the game, it will usually be on a drive change.
Also keep in mind that the offensive formation affects which players are in the game as well.