You'll create the animations in Blender. Which is good, because it's a lot easier to make sure things match up right there in Blender where your assets are being created.
The animations (including bones/armatures) will export to Godot 3 and the animations will show up in the Godot AnimationPlayer which is automatically created in the node stack when you do your import. Works pretty clean.
Just make sure when you do the Better Collada Export from Blender that you (at least) select both Armature and Mesh, and check the boxes for "Export Animation", and "All Actions"