Assuming Submerged:
Superb: Deceit
Great: Alertness, Stealth
Good: Fists, Athletics, Contacts
Fair: Driving, Endurance, Guns, Investigation
Average: Discipline, Rapport, Presence, Empathy, Burglary
You might want to shuffle some of the skills to suit your preferences. This arrangement is meant to represent someone who is a sneaky type spy, with good physical abilities to back up the sneakiness. Alertness seems to be a natural pick for a high skill, because you want him to be able to quickly recognize hidden threats and avoid being ambushed. Contacts is another useful skill for this type of character. You might want to put craftsmanship in there if you want him to be the type to make his own gadgets.
Consider getting stunts from the options listed in the book for the following skills: Alertness, Athletics, Deceit (Make-up artist is especially suitable), Endurance, and whichever skill you plan to use most when attacking.
