I use the ebook library, drag and drop to the main library, then from there to the Reader. Then I put the books on the Reader into collections.
The advantage to this is that the formatting seems to be done during the transfer process, and not on the Reader when you try to open the book (at least, I've never seen that before).
As a note, on my last set of book uploads the behavior was mixed: adding book to the library and transfer were slow again, the organizing of collections was fast, and the formatting delay was not seen for those books. So I presume it's a difference in the transfer itself.
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