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There is a calibre companion for the iPad in the Apple app store. That's what I use. It works well for me. Unless you hack your iPad, all apps are downloaded from the Apple app store. Some people call it The Walled Garden.
Marvin will connect to Calibre, but it doesn't do PDF.
I believe that if you have multiple apps that support PDF, you will be presented with a selection, if there is only one app, then if opens up automatically. iBook understands PDF's and is built into the iPad, but many people prefer Goodreader, which you can download from the Apple app store.
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