OK, so there's the specific list of skills (Gunnery, Negotiation, etc). Figure your bonuses for those. Discard any points in the lower of either Pistols or Rifles, and any points in 2 of the 3 Gunnery Skills. Any EXTRA points from your specific skills are totaled up, cut in half, and added to your "free point pool".
Add up ALL THE OTHER POINTS. Divide it in half. Those are your "free points". They can be used to increase skill ratings in the specific skills. The other skills (Academic, Perception, Sensor Ops) don't get used at all, so you get some of those points to widen your skill set.
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Example (* denoted tracked skill) (There are no Traits in play in the example)
At the end of character creation, Sample McCharacter's skill points look like this:
*Gunnery/Ballistic - +13
*Gunner/Laser - +3
*Gunnery/Missile - +3
*First Aid +9
*Negotiation - +8
Academic/History - +5
Computers - +3
Gunnery/Ballistic is higher than /laser or /missile, so that's what is used to determine our Pilot's Gunnery Skill. /Laser and /Missile are discarded entirely. A +13 in Gunnery/Ballistic is enough to generate a +3 modifier, with 0 points left over. First Aid is also a tracked skill, and 9 points is enough to generate a +2 score with 2 points left over. Finally, Negotiation generates a +2 score with 1 point left over. There are 3 points remaining from our tracked skills. Half of it goes into our Free Point pool, so we add 2 points. Our skills look like this:
*Gunnery - +3
*First Aid - +2
*Negotiation - +2
FREE POINTS: 2
Next, we add up the number of points from untracked skills. A 3 in Computers and a 5 in Academic/History total up to an 8. Divide it in half and add to Free Points. 8/2 = 4. 4+2 = 6. Our skills look like this:
*Gunnery - +3
*First Aid +2
*Negotiation - +2
FREE POINTS: 6
The Free Points are now spend to increase Tracked skills. It costs 7 points to buy a +2 score, and 13 points to buy a +3 score (with no Traits affecting anything). The difference is 6 points. We'll spend all 6 of our Free Points to increase our Negotiation Skill from a +2 to a +3. Our final skills look like this:
*Gunnery - +3 (A 5 Gunner on the tabletop)
*First Aid +2
*Negotiation - +3