So in short words, only one tree is active in each world, to find the location of the active tree right click a crystal tree and chose the option "look at" if it is the active tree it will say "This tree points to the heavens." else it will say "The tree leans slightly towards the [direction of the active tree].", so you'll know which tree is active by the message below is a map with all the trees.
Here is an example:
"Little happy Lilly decides to cut crystal trees, she teleports to seers village and goes check the crystal tree north of the flax field, she looks at the tree and the tree says "The tree leans slightly towards the west." lilly takes a second and suddenly a lamp appears on top of her head and she screams "The tree is in the tree gnome stronghold near the gnome ball field! I must get a magic log and travel on a balloon!" and there she happily goes cut a crystal tree."