This is something I would really love Spine to be able to eventually do someday: Have multiple bone hierarchies and switching between them within an animation, within one skeleton (at least without the associated cost of having twice or thrice the number of bones being updated or having a bunch of extra timelines keeping slots enabled or disabled per switch to a different hierarchy)
Sadly, this isn't ideal or efficient right now, workflow-wise and performance-wise, even if it is possible and even playable given enough CPU power.
And for anyone else reading and knowing that this isn't as big an issue and I think, let me know.
Here's how it works now, assuming this is a Zelda-like game:
(1) The artwork/images don't need to be separated. You can put them in different subfolders, but they can all be in one atlas, SHARED by three or four or as many skeletons as you need. So if you ever need to use one image across all skeletons, it's not a problem at all.
(2) A Spine project can have multiple skeletons. This means you have one .spine file and can see them and animate them in each others' context. If you already started working on different skeletons in different .spine files, you can use the Import Project option under the Spine menu to bring the different skeletons into one .spine file.
Given (1) and (2), you can expect one .atlas.txt, one.png, and several .jsons going into Unity.
(3) This will take more thoughtful programming than if it were a sidescroller. What you'll need after this is an intervening class that knows what state your character is in and handles which skeleton to show or hide and play animations from when you, for instance, press right, or press up, or attack.
(4) Sadly, since the three or four directions will be segregated into their own skeletons, this will make it very weird to make animations that make your character spin around these directions (as Link usually does with special attacks).
PS
This is also assuming you're actually using bones to animate these things. If you were just using frame-by-frame animations, this isn't an issue at all.
