If you're interested in reading about A*, the best documentation I've ever found was this article on Gamasutra:
http://www.gamasutra.com/features/19990212/sm_01.htm
It explains the differences between pathfinding algorithms in such a simple way even a kid would understand.
The article requires a login to Gamasutra ; you can safely create an account, they won't sell your email to spammers like Gamespy does. And there are tons of interesting articles to read there.
In the end I believe waypoints should be distributed evenly all around the map, in all places a player could go, with perhaps a little more density on the most tactical zones and less density in wide open spaces where nobody ever goes. It's the A* pathfinder which will evaluate the best path given the domain knowledge the bots have of the map and the danger of each area. It won't necessarily be the shortest path always, but rather a weightened compromise between shortness and safety.