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I think the original poster is asking how he can decide which books go into main memory and which onto the SD card, using Windows Desktop Mobi Reader to load books.
The answer is "you can't". Mobi Reader allows you to specify a single sync location, and that's where the files go.
My advice would be to forget Windows Mobi Reader and load files manually to the Gen3. Simply open a Windows Explorer window on either the drive labelled "Gen3" (which is the internal memory) or the "SD Card" drive (the Gen3's SD card) and simply copy files from your computer to the "ebooks" folder on the appropriate drive.
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