ha, that is the million dollar (euro...) question, indeed.
personally, i only did a batch import once, because there is usually a LOT of retouching to do by hand in order to get the meta data displayed correctly. my favorite shortcut in calibre is E for "edit metadata". since then i import one by one, which is more fastidious but also avoids those infuriating mangled entries where the meta data is missing or wrong.
for series, you can include it in the title if you like, that way you are sure to see it once it's on your device. however in calibre i recommend you *also* use the dedicated "series" field which allows you to name the series and then indicate which volume it is. you can then sort by this field which is very convenient, and like tags it will create a collection on the sony. i use the comments field for a description / summary of the book and any other pertinent info ; the sort of thing you find on the back / inside cover, or in the amazon page. for almost everything else you can use tags. i use tags sometimes for category (obvious use) but also to specify if i've read the book or not as this allows me to sort them by read vs. unread. little tip, tags created in calibre will automatically create a "collection" when you send the book to your sony, so you can look in the collections page and choose by "mystery", "news", etc. corollary, don't create too many tags, or you will have eleventy million collections on the sony.
let us know what good ideas you come up with yourself, i'm always interested in better ways to organise my books.
