You pick a specialty *every time* you gain a rank in the general skill.
Example:
Before any character generation takes place, the Engineering skill tree looks like this
Engineering/Jump Drive: -- (no skill, penalty on all rolls)
Engineering/Maneuver: -- (ditto)
Engineering/Electronics: -- (and so on)
Engineering/Life Support: --
Engineering/Power: --
If you were to gain a zero rank, such as in Basic Training, it now looks like this
Engineering/Jump Drive: 0 (no bonuses or penalties from skill)
Engineering/Maneuver: 0
Engineering/Electronics: 0
Engineering/Life Support: 0
Engineering/Power: 0
Once you gain a rank, it needs to go to a specific spot. Even if you didn't go through the "zero" step explicitly, it still happens once you get a '1'.
Engineering/Jump Drive: 1
Engineering/Maneuver: 0
Engineering/Electronics: 0
Engineering/Life Support: 0
Engineering/Power: 0
If you gain another rank, it can look like this
Engineering/Jump Drive: 2
Engineering/Maneuver: 0
Engineering/Electronics: 0
Engineering/Life Support: 0
Engineering/Power: 0
or like this
Engineering/Jump Drive: 1
Engineering/Maneuver: 0
Engineering/Electronics: 1
Engineering/Life Support: 0
Engineering/Power: 0
And so on.