When you beat the game on normal you unlock the Estovakian color set. The 3rd set is aquired by shooting down the named aircraft in Expert. You unlock 1 paint scheme for every plane you shoot down.
To get the second color for the cfa-44 you have to buy every plane and every color of each plane, then play and finish a mission.
To unlock the third color scheme for the CFA-44, have all "S" ranks in all missions from the Easy through Ace difficulty settings, earn all Operation Medals, have at least 15 Service Medals, have all Enemy Records, and have all Friend Records.