You don't have to use multiple atlases when images don't fit in one atlas page. You can use a single atlas with multiple pages. Use folders to control which images are grouped together on the same page.
Can you explain the technical reasons why you split a skeleton into multiple? It may help us give advice and in general it's helpful for us to understand why users do what they do. In most cases it's better not to split a skeleton into multiple and there are some workarounds depending on what you need to do.
krutovig I need to pack atlases separately, export goes to the different folders, so each time I change anything I should unmark export for all those already marked and then mark necessary ones.
Packing atlases separately from data export is good, though unrelated to exporting all or one skeleton.
It seems that the main issue is your skeleton exports go to different folders?
We recommend using a build script to do your exports. You could have a script that packs images and puts them in the right place, and another that exports skeletons and puts them in the right place. It wouldn't try to export just one skeleton, it would just export them all and put them all in the right place. That's usually very fast and it's not worth optimizing it to only export a single skeleton.
Your script that packs an atlas could copy images from multiple places into a temporary folder to get the folder structure you need, then pack that. This allows you to control how things are packed even if you want to use a different folder structure in your skeleton images folders.
Using a script has many advantages. You ensure your builds always have the latest exports and it makes upgrading to a new editor and runtime version very easy.
