You can sort your collections by author, title, order or date. In calibre you can set the order using the "series" tag. I don't know what you do with the sony software, I don't use it to make collections.
You can't set margins on the reader, it depends on the ebook. Again, I think prs-900 has an option to remove margins for pdfs.
No problem with meta data as far as I can tell.
The lighted cover works great for me when it's dark. The reader is perfectly readable when it's bright. When the illumination is dim however, the glare and reflection are a bit of an annoyance (as is the low contrast), and the cover light is not strong enough to solve that. The problem goes away with changing the angle of the reader or ideally, illuminating more brightly.
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