As you can see, when I import it there are no bones in the mesh. (I exported it from Blender as a .fbx file with Apply Scalings set to FBX All). There are no clear tutorials i’ve found on this, so any help would be appreciated!
You need to ensure that both your cubes are joined together into one single mesh. Then you need to parent your cubes to the armature by doing Ctrl + P > With Automatic Weights