The "default" AIs (especially the Beta Agent) are set up to be as optimal as possible, but playing around with the characteristics could yield interesting results. If you are playing a game with several AIs, it may be worthwhile to make some slightly more aggressive and some more defensive, to simulate actual differences in play styles.

Let us know if you find settings that work better than the default, we would love to improve the AI however we can!

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There's not a manual on it, but I'll list a few tips:

* Use Beta Agent; it's generally the best. Vigilante is very similar. Use "Lazy" if you want AI to make the fewest possible actions (similar to 2-player version of board game Risk)
* When you have a list of agents customized, you can save/load it in the players dialog. So if you take Smiley's suggestion you won't have to edit the values every time.
* You can look at the source code if you want to know exactly what something does.
* Beta Agent has an evaulation function for territories: if a territory is more "valued", the AI will be more likely to attack/nuke it (if unowned) or defend/reinforce it (if owned). Many of the values affect the evaluation of individual territories. For example, "LockedInValue" is a modifier applied if a territory is "locked in" by friendlies and thus doesn't need to be defended (default is -30). LandingSiteValue helps defend landing sites (default 6).
* The values you might try messing with first are MinAttackMotivation and MinAttackStrength. MinAttackStrength is the minimum units required in a territory for attacking: so if MAS is 6, the AI will never attack from a territory with fewer than 6 units. MinAttackMotivation is more complicated, but basically a lower value makes a more aggressive AI, and higher value is more conservative.
* The MinEnergy values affect how much energy the AI will stockpile. Lower values mean it will spend more.
* SpecialUnitMultiplier = how much AI cares about commanders/gods/temples/etc. Higher value makes it protect them more.
* The Min/Max RandomAttacksPerTurn cause the AI to randomly attack... it can throw a wrench in things if they are too predictable.

Hope this helps :)

Any way to set AI players to be on the same team? That might make single player games more challenging :)

Not without a little programming ;)

However, you can play with Vigilante and set his Vigilantism factor higher. It's identical to Beta Agent except that it should be more likely to attack the player with the most territories (and less likely to attack someone with fewer). I'm really not sure how well it works :S