@geoffenzed - Correct on all counts. They are listed as "Skill 1" - so if you have it, then taking the skill doesn't help. Specialties count as different skills - You'll only ever have Pilot 0 and when you earn a 1, it becomes Small Craft 1 or Spacecraft 1, etc. :)
The Skill packages are intended to round out the party's missing skills, not to level up stuff. That's why they are listed with the 1.
So, pick an order and start picking skills.
@Knighthawke - have you had a chance to fill in a character sheet. Can you submit it when it's done?