The base spy skill is random 1-3. They get bonuses from Thieves Guilds (make sure you have patch 1.2 which fixed some thieves guild bugs), but other than guilds or sending them on missions, the only control you have is to get them ancillaries:

Code:
Beguiling Bard	+1	5%  Spend turn in city with Brothel
Dancer		+2	5%  Spend turn in city with Brothel
False Documents	+1	33% Spy on city under revolt (or cause revolt?)
			33% Recuit in city with Printing Press
Pickpocket	+1	12% Recruit in city with Market
Pet Monkey	+1	5%  Recuit in city with Market (not avail. in Europe)
Notes:
'Brothel', 'Market' means that level or better.
Other effects besides Skill:
Bard gives +1 against assassination; Bard, Pickpocket give +1 LOS; Recruiting in city with Dockyard gives 20% chance for Spyglass +2 LOS.
All info is from http://noctalis.com/dis/totalwar/m2tw_agents.shtml, an EXCELLENT reference for all agent/general/princess traits, it's not totally complete but it is a lot easier than digging through the data files.