I do not have my N7, but from what I have read the N7 will be recognized as a "Portable Device" in the Windows environment, if so Calibre will not recognize it as an e-reader and allow you a direct transfer from Calibre, much the same as my ThinkPad Tablet. Also even though the Portable Device in Windows shows up as a drive, you may not be able to see all of the folders, much as the OP (Original Poster) noted that they could not see the ebook folder. This is understandable because the device is designed to purchase books from the Google Play Store. First off the native e-reader may not allow you to view non-Play Store Books, so you may have to go to the market and install another e-reader like Aldiko
. You can copy your books to the internal storage of your Nexus 7 with the Windows file explorer and create a new folder and place them in an existing like music or pictures, if you have write permissions to those folders. Then you can use a app like Astro
file manager to move the books to the folder that you wish and have them show up in your e-reader. You will note that with the Astro file manager you will be able to see all of the folders that were not visible in Windows. I would expect Calibre to eventually allow direct communication with Windows Portable Device or WPD and since I do not have the latest version of Calibre it may have been implemented in the latest version. I have successfully copied books to both of my other tablets, but without the N7, I can only give general guidelines at this point.