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If I remember correctly, the collections information is not stored in the ebook file.
Upon exporting from Calibre or the Sony software, the collection information is added into the reader in a database of some form (I think) that the reader can read. This is due to an ebook being able to be part of as many collections as you like without having to have more than one copy of the ebook on the reader.
Any series information that you may be able to store in the ebook file itself will be ignored by the reader.
As to formats: Epub is a good choice and Sigil allows you to edit the file without having too much knowledge, even beginners can make an epub with Sigil. Being as it's XHTML based, then with a minimum of HTML knowledge, you can improve the look of the Epub in Sigil's code-view or just stick with it's book-view and use it like a word-processor.
Due to you having a Sony reader then full justification doesn't work on the screen with stock Sony firmware's installed, but you could update it with a custom firmware to get this functionality.
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