There are a copule of ways to get books from Calibre's content server into ibooks.
The first way is simply to use Safari to navigate to your content server and then when you download the book do an "open in ibooks".
Another way is to use a free app called "ebook search". You can add the opds feed of the content server to that app and then also do an "open in ibooks" to get the book into ibooks.
Both work well, though the latter is a little easier from a touchscreen device.
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