I see that California Classics' 1950s AI packages have been mentioned (they have both civil and military packages, though I believe the military package is only MATS cargo planes.) If you like the really old stuff, there's Golden Wings, which includes period AI for the entire FS world.
For modern military AI there's the Military AI Works packages.
Cal Classics offers a split version of the FS9 traffic file that separated the airline and GA traffic into separate files. That's handy if you want to ditch the stock AI airline traffic and replace it with an add-on without losing your GA traffic.
There doesn't seem to be any limit to how many traffic files you can have, so you can create your own AI schemes and have it in separate files that you can activate, inactivate or change without affecting anything else.
To answer your questions, as has been mentioned, AI planes live in the Aircraft folder with the flyable planes. They don't show up on the select aircraft menu because they're coded as AI types in the AIR file (Aircraft type=2; you can open and edit AIR files with AirEd.)
Some (not all) AI planes can be made flyable by adding a panel and sounds, and changing the aircraft type code to zero. Most (not all) flyable planes can be used for AI. You can make an AI version by stripping out the panels and sounds (AI uses a separate, generic sound set from the main FS9 Sounds folder), or you can just use the flyable plane for AI.
You would create a new AI plane the same way you'd create a flyable plane, except that you wouldn't need a panel or sounds. The flight model might be different for some planes, but I don't understand that part in detail.
As has been mentioned, if you want to do more tan add packages (which generally only populate the larger airports, or at least only those that Microsoft has provided with AI parking - which is mainly the larger airports) you'll have to learn to use Traffic Tools and AFCAD. Both of those programs come with comprehensive instructions that will teach you all you need to know about using them and about AI. You'll probably also want a flight plan editor like yRoute or AI Flight Planner; manual writing and editing of flight plans is extremely tedious.
Have fun!