Multiple SkeletonData assets can share a single Atlas asset.
If everything fits in a single atlas, just assign the "Atlas Assets" field of all your SkeletonData assets to use the same single atlas.
The only thing you have to handle is making sure none of the images from different atlases have the same name or they'll collide when you pack the new single atlas. If you opt to resolve this collision by putting the images in subfolders, you need to make sure each skeleton uses the paths that include the subfolders.