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Most books from itunes have Digital Rights Management which is like a lock wrapped around the file to stop editing and copying. I don't think you can open a DRMed book file in Sygil.
When moving a file to iPad you don't put it into a folder. You open iTunes with the iPad plugged into the USB port. The iPad will show up in the left column under Devices.
Click the iPad. Select Apps in the other panel which shows the apps installed on the ipad and scroll down until you see the app you want to add a book to. With the app selected, drag the file you want to add to it to the list next to the app.
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