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Are you using CC as the device? If so, then no, all books are considered to be in "main memory" no matter where they are really stored on the device. CC ensures that the books are stored where you ask.
BTW: I suggest that you put the books in a subfolder on the SD card. Otherwise every time you connect, CC will scan the entire SD card for books unless you turn off scan on connect. Putting the books in a dedicated subfolder ensures that CC scans only the folder(s) of interest.
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