Thanks for the reply!
So that would allow me to animate them both at the same time inside of Spine. I believe that would mean each skeleton still has its own set of animations and it would be up to my engine to sync the animations for all the skeletons (which is what I'm currently doing).
What I was hoping was that I could have one single animation that animates more than 1 skeleton in order to easily have the skeletons interact without having to skip backwards and forth making sure that all the animations sync up together. Importing them seems to make that job a little easier, but it still means I have to call play on each skeletons animation rather than triggering one single animation, and my engine making sure that the skeletons are in the correct positions to start with.
I'm guessing the only way to do this is to build a spine file specific for the cutscenes which includes all the characters bound to a single root bone.
Thanks anyway, I'll keep messing around with it. Despite me still learning, I do find myself actually enjoying animating - it used to be such a chore! =)