Specialties are not separate skills (and, thusly, do not have separate ranks). They are part of the main skill, and provide a +2 to the character's roll for tests involving the specialty.
Using your example above, the character has two ranks of Systems Operation (Tactical) and three ranks of Systems Operation (Flight Control). This means that, in Coda, the character has five ranks of Systems Opertaion, with specialties in flight control and tactical.
Ignoring attribute bonuses, the character would receive a +5 to his 2d6 test roll for general systems operation tasks. For tasks dealing specifically with flight control and tactical systems, the character would receive a +7 to the test roll.
Davy Jones
"Frightened? My dear, you are looking at a man who has laughed in the face of death, sneered at doom, and chuckled at catastrophe! I was petrified."
-- The Wizard of Oz