I am pretty sure the apnx files are for the page numbers. There is also as far as I can remember a file with bookmarks and the last page read on the kindle as well.
As far as the books being poorly formatted, calibre can often fix poorly formatted ebooks if they are not DRMed. This takes a bit of practice on the users part but is well worth it.
One of the nicest things about ereaders and calibre is that 99% of my books are formatted according to my preferences. The hardest part was figuring out what my preferences are.
Helen
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