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You mention Magic ISO, but I am not really sure what you mean. An ISO file is generaly an exact image of a CD or DVD. Are you saying that your books are in one of these files? An ebook is normaly just one single file which can be dragged straight to the ipad via iTunes. Most ebook files these days are epub files and their file names end in .epub
It might be that your books are ZIP files or in compressed formats, and because you have Magic ISO installed on your machine, it is that that is opening them by default. If this is the case, then within those ZIP files will be your ebook files.
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