Maybe. Depends on the eBook reader.
If you are using iBook eBook reader, then iTunes -> Books, then you should be able to drag and drop the book onto your iTunes icon, or you can use iTunes -> File -> Add to Library...
If you are using a different eBook reader, then it may have registered with iOS that iTunes may sync documents for the app.
iTunes -> iPod Touch -> Apps -> File Sharing. Select your App from the File Sharing list, and drag your ebook to the Documents window.
eBook readers I know that support iTunes sync'ing are
This is NOT a complete list, just the eBook readers I have installed that show up under the iTunes File Sharing section. Stanza being my preferred eBook reader.