Hiya!
Ahhh...Greyhawk!
Been DM'ing in it since '82? I think that's when I got the Folio. Anyway...
One thing to keep in mind about Greyhawk is that there is a LOT of "open wildlands". Another important thing is that Countries tend to be fiercely independent and fairly nationalistic ("out country is the best, obviously, but we'll still trade with our neighbours...because, well, we like to help folk less advanced as us"... that kind of thing). Because of this, any successful organization that spans more than the home country (or even city!) needs to be quite secretive (e.g., Scarlet Brotherhood, for example).
What I have done in the past is start with a "home base". This is the core city that the 'faction' (guild, cult, society, whatever) originated in or has it's main leadership. Then, I simply start moving outward along the road and water ways to nearby towns. I add a little blurb in that town's write up about the 'faction' and it's goals for the area. Then move to the next settlement, and make another note. Eventually I arrive at a settlement or border or some other barrier that seems it would be hard for the 'faction' to traverse with any regularity and that's that.
The reason I build it this way is that it feels "Greyhawk'ish" to me; nobody really has any Flanaess-wide reach other than an EXTREMELY limited selection (Scarlet Brotherhood, Circle of Eight [still Circle of Eight in my game], perhaps the Iron League to some degree). It also allows me to utilize one of the major features of Greyhawk; to be able to add a whole "Evil Society of Evil-Doers Doing Evil" in some town/city/area and not have it conflict with anything canon. As I said, there is a LOT of space between towns in Greyhawk, and the generally 'contained' countries, a DM has a HUGE range of freedom to do what he/she wants without stepping on any previously detailed "creative toes". The same can not be said of other, shall we say, more contemporary worlds nowadays.
So, my suggestion: DO NOT think "world spanning". Think small. At most think "country wide". Then you just play your game and keep doing all that behind the scenes DM stuff. Eventually the players will have their PC's either FUBAR said 'faction', or said 'faction' starts to get attention from other factions that are in the countries that they are now trying to influence....enter gang-wars. If you create a more "world spanning" or "huge" faction that is known all over the place, you will be doing your players and yourself a disservice in potential PC-world-shaping.
^_^
Paul L. Ming