Hi leneleeb
I've just tested it, and ATUM is preserving the variations order by default in Stock Central.
This was the initial order:

And thereafter, I went to the variable product, reordered them with the drag and drop functionality, and went back to Stock Central:

But please note that this only happens if you don't use any column sorting by clicking any of the table headers.
If you, for example, sort by product name, all the variations will be sorted alphabetically together with the first-level products.
I hope this helps.
Best Regards,
Salva.