Yes, I agree the manual is not very helpful for scenario designers. When you click units, a large bar comes up on the left side of the screen listing all units you can place for the different players. Change the player from "Player 1" to "Gaia" and you will be able to place all of those lovely little things that make maps look better.
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I am the lone gunman,
I am the super Fool,
And when I laugh, the earth will shake,
And you shall know my rule. -sF