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I'm assuming you have sync turned on and this will probably need to be turned off.
To the best of my knowledge the Sony software does not have any type of "playlist" to help sort between your titles and your wife's titles. You will just have to remember which ebooks are yours when copying to the Reader.
An alternative is to use Calibre to manage your library. You can 'tag' each book to help with sorting and easily see which ebook is yours and which ebook is hers.
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