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Where you put the books shouldn't matter. About the only thing is not to put them in a folder that starts with a dot as the name. The other is to make sure they have legal file names, but using calibre should make sure of that.
When you disconnected the device, did it show the processing screen? This is a black screen that shows it is processing the books and adding them to the internal database and hence the library. If it didn't show, then check the books where actually put on the device.
If the processing screen did show, then it probably means one of the books is bad in some way. When the books are first seen, they are processed and added to the database. If this fails for a book, other books in the same batch are not added. Unfortunately, the only way I know to find the bad book is trial and error. You will need to remove all the books that didn't get put into the library, and add them in small batches or one at a time, until you find the one that didn't work.
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