The extra resources are specific to the scenarios; e.g. stone in the Middle Ages. As far as I know (maybe someone can correct or clarify) the game only allows eight strategic and luxury resources, so you can't include stone, wool, etc as extra strategic etc. resources. But there isn't a limit on the number of bonus resources.
To include them in your game, use the editor, but again, I'm not familiar with the precise mechanics of this. Also, check out modpacks like Double your Pleasure (DyP) to see examples of many bonus resources.
