Say it with me: “The GM has the final word!” Good, I hope that helps; it certainly makes me feel better. The rules for a campaign the size of Living Greyhawk seem quite bewildering at times and keeping up with all the minutia of the D&D core rules is a daunting task especially if you don’t know where they begin and where they end. Since GMs have the privilege of making decisive rulings during game play, it's important to understand where to go when looking up rules.
Your first source for rules is the current printing of the three D&D core rule books: Player's Handbook, the Dungeon Master's Guide, and the Monster Manual. This trio of books forms the foundation of Living Greyhawk, and they are only trumped by the few sources listed below. For the most part, these books are the law of the land and your primary concern.
The next official source for the rules of the game, used by the Living Greyhawk campaign, is the D&D FAQ, or Frequently Asked Questions document. This document, maintained by Wizards of the Coast, contains clarifications and errata solving 90% of the problems you might encounter while running a Living Greyhawk adventure. The FAQ document is updated a number of times per year and is official for use in the campaign.
Your last source for official rules, while running a Living Greyhawk adventure, is the Living Greyhawk Campaign Sourcebook (or LGCS). The LGCS contains all the rules needed for character creation and advancement, but it also adjudicates some of the rules unique to the campaign and clears up some problems that occur due to the nature of the play environment. The LGCS trumps all other sources in this regard and is released roughly once every six months with new updates.
Even with all of these official sources of rules knowledge, it is still pretty easy to run into a situation that falls outside these guides. As a GM for the Living Greyhawk campaign it is your job to make the final call. There is plenty of help out there to get you through the rough spots, and while not official, they can certainly be used as guidance to make the call when the rules are unclear. Game magazine articles like Sage Advice and Rules of the Game both are great sources of advice, and while they are trumped by official rules, they can really help through the tough spots.
As an example, Regdar the fighter is crossing a chamber filled with water up to his shoulders. Half way through the chamber, an evil wizard appears on the other side and lobs a fireball into the chamber hoping to fry poor Regdar. Now, the simplest way to deal with this situation is for Regdar to roll a Reflex save to determine his fate, dealing damage normally, but this does not seem very fair to poor Regdar who is in shoulder deep water. Looking into the PHB gives little guidance as the fireball spell description does not cover this situation. Next, looking into the DMG gives us a little bit of help. Here it mentions that a fireball cannot be used underwater without a successful Spellcraft skill check (DC = 20 + the spell level). If this check succeeds, the fireball will function underwater and Regdar is toast. However, it’s made pretty clear in the discussion of line of effect concerning fire spells and water that the spell has to be one or the other, above, or below water. Our bad guy, being above the water has to center the spell above Regdar’s head. So, we are right back where we started. Next, looking to the FAQ we find no help there and the LGCS provides no guidance either. Running out of option, it’s time to make a judgment call. Using the cover rules presented in the DMG, we can infer that the water gives Regdar cover, providing him a +2 cover bonus to his Reflex save. The next better option is to give him improved cover, giving him a +4 cover bonus to his Reflex save and improved evasion against the effect. Since Regdar is up to his neck in water, I would go with the improved cover version.
Regdar rolls his Reflex save with a +4 bonus, makes it and takes no damage having ducked under the water. By the time he comes up for air, the evil wizard is gone, but Regdar chases on with a score to settle. Meanwhile, you as GM can keep the story moving, knowing that right call was made.