Easy peasy........if I understand you correctly.
I have mine sorted by series, in chronological order also....here is what I do.....
In front of each title I put "1", "2" etc. Now, under 'edit meta data', see where it says 'series? Enter the total number of books in that series...if you don't know the total, go to
www.fantasticfiction.com
enter your author, and you'll see.
Once you've entered "10", or however many books there are, you can enter which number this particular book in the series it is......book 1, 2, etc.
Do this for all the books in the series, then click (at the top) "series" then "author"........this should put them in the correct numerical order.
when I load mine on my Kindle, as long as I load them in the proper order, they show up in the proper order.
Hope I've understood you correctly, and that this helps.