The different formations build an approximation to a stone-scissors-paper princible: Stone beats scissors, scissors beats paper, paper beats stone.
Important: "Beats" just means that you have a small advantage if you play the counter formation. This means that you win roughly 1 more game out of 10 if you play the correct counter formation. Over a complete league season, this can sum up to a couple of points.
The system works as follows:
Stone = 4-4-2, 4-3-3 and 4-2-4 (offensive)
Scissors = 3-4-3 (causes less counterattacks due to ball possession, but weak against offensive teams)
Paper = 5-4-1 and 4-2-3-1 (win with counter attacks against offensive teams)