On the civilizations tab, you can set priorities for the AI when it's playing that civ - telling it what to concentrate on building, etc. You can also set the aggressiveness meter, but I'm not entirely sure if this is even used by the game, or how much. Basically, the AI check boxes on units allow you to associate certain units with certain AI strategies, so if you create a new unit you can classify it so the AI will know when to build it and what to do with it (for example, classifying a new Super Flamethrower Nuclear Missile Terrorist as an offensive ground unit so the AI doesn't build them when it wants to make roads. Instead, it will build 500 of them and have them continously patrol its borders). The editor 'assumes' things for you, like that you wouldn't set an artillery unit to be used for exploration (since it can be captured). This also helps prevent you from tricking the AI into doing stupid things with the units. Personally, I don't like how the editor 'assumes' things like this for you, but technically it makes sense.
Hope this helps,
SpaceWeasel