You receive perk points by killing other planes or destroying objects in the MA.
All planes have ENY values and all bombers and ground objects have OBJ values. When you down another plane, the perk points you receive is calculated by dividing the ENY of your plane with the ENY of the downed plane (thus better planes have lower ENY, and you get more points for downing better planes, or for flying crappier planes). If you're flying an attack sortie, you are awarded points for the damage you deal to ground targets based on your OBJ value and the target OBJ value. Landing a sortie multiplies all points you earned in that sortie by 1.25.