Hello there, and sorry for the ridiculously long huge gigantic delay with the reply.
If I understood you correctly, you seek the functionality which will allow you to move Sprites along with the Regions inside an already existing Atlas (created by packing) and also to pack new ones without disturbing or re-arranging everything that's already there?
If so, then it would make an interesting feature.
Sadly, Atlased doesn't support such workflow at the time.
To make it possible, a decent amount of work needs to be done on built-in Sprite Packer and/or Atlas data format itself.
I will probably try to come up with something in the future versions.
Sorry again for the inconvenience.