Here is the rule for the ranking of the teams in the Group Stage of the World Cup, from Article 41 of the Regulations, 2014 FIFA World Cup Brazil (PDF):
This rule concerns how the teams are ranked after the Group Stage (Round of 32) is done, determining which teams move on to the Round of 16.
In each group, there are four teams. During the Group Stage, each team plays the other three teams in their group. For these three matches, each team is awarded 3 points for a win, 1 point for a draw, and 0 points for a loss. After the Group Stage is over, the four teams in each group are ranked according to how many points they accumulated over the three matches. (This is criteria A in the rule you cited.)
If there is a tie after this ranking, criteria B and C are used, using the statistics from ALL three group matches that each team played in determining the rank order.
If there is still a tie after criteria C is applied, criteria D, E, and F are used. The difference between these three criteria and criteria A, B, and C is that with D, E, and F, the only match(es) you look at is the match between the teams that are still tied.
After the ranking in each group is figured out, the top two teams in each group move on to the Round of 16.