This is an old, or at least an old-ish topic, but I'd still like to add my 2 cents in case it'll be useful for someone in the future.
To set the animation you need to access the AnimationNodeAnimation. You can find it through the TreeRoot. If you use, for instance, the AnimationNodeBlendTree as the root in your AnimationTree, then you just use GetNode to get the AnimationNodeAnimation that is used to select an animation with SetAnimation.
In C# it'll look something like this (assuming you're using a blend tree as the tree root):
// Get the node from the scene
AnimationTree animTree = (AnimationTree)FindNode("your_anim_tree_name");
// Get the tree root using the correct type
AnimationNodeBlendTree animTreeRoot = (AnimationNodeBlendTree)animTree.TreeRoot;
// Find the animation node from the tree
AnimationNodeAnimation animNode = (AnimationNodeAnimation)animTreeRoot.GetNode("your_animation_node_name_inside_your_blend_tree");
// Set the animation
animNode.SetAnimation("some animation");
So if I have a blendtree and inside it an animation node called "Animation_Upperbody_Idle", I'd use that as the ID in my animTreeRoot.GetNode-call.
If you plan to use the scene you're animating as a template to, say, instantiate a lot of baddies who all run a different animation at any one time, don't forget to check the "Local to Scene" checkbox for your animation tree nodes. If a node is not local to scene, all the instantiated nodes will share the same node. What this means is that if the "Local to Scene" is not checked on your animation node, when you change the animation to one baddie, you change it for every one of them.
