I'm not completely sure what you want. You mention series, chronological order and and "incremental id in the bookstore".
Taking the last one, I think you mean the id number calibre uses. If so, this is just incremented each time you add a book. It doesn't really mean anything, but, is used internally for lookups and things.
For a series, the series index is used for the order. If you don't do anything except add a book to a series, it will just increment (though there are tweaks on what to do). You can reorder the series by changing the index for the books to whatever you want. Just edit them. Or, use the metadata download to get them from an on-line source. There is also the Manage Series plugin. That you can use to reorder books in a series in one go.
For chronological order, it will depend on what you mean. If you mean publishing order, then you can set that in the metadata and sort on that. If you mean chronological in the series, then it is probably simplest to set the series index to represent this. Or add a second series column if you want to maintain the chronological order separate from the series order.
The above is what your post suggested to me. Hopefully it will help. But, I feel I might have missed something. Can you explain a bit more what you want?
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