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Put them anywhere. You'll have to use your reading app (Kobo, Aldiko, etc., etc.) to import the file and add it to their library. If you place it in there manually, your app'll either choke on it, make a duplicate (but renamed and put into what the app considers the proper directory structure), or import it and delete the original. I have no idea which 'cos it seems to vary based on the app, the phase of the moon, and how annoyed at me my Arc is. :P
Personally, I just dump them into the download directory so that they're easy to find and delete if they're still there after being imported into the app.
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