Profession. Mostly.
Each of the Basic Professions and the Starship Officer Elite Professions have, as part of their descriptions, two little sections entitled "Attrubutes" and "Reactions". They may be found in the Game Information section of the profession's description, right before the Professional Abilites.
These detail the favored Attribute and Reaction for the profession (Starship Command Officers favor Presence and Willpower, while Soldiers favor Agility and Quickness, respectively). They also make suggestions for the second favored attribute, based on what else would be useful to the profession (such as Agility and Vitality to help keep your Command Officer alive; or Strencth, Vitality, or Perception for the Soldier), but these are merely suggestions so if you really want your Soldier's second favored Attribute to be Intelligence (or Presence), go ahead.
Hope that helps you.
-Chris
"Was entstanden ist, das muss vergehen. Was vergangen, auferstehn." -Klopstock & Mahler
"Only liberals really think. Only liberals are intellectual. Only liberals understand the needs of their fellows." How much viciousness lay concealed in that word! Odrade thought. How much secret ego demanding to feel superior. - Heretics of Dune