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For reading pdf's the standard reader is best I think. But I'm not sure for annotations. I don't think it's able to merge annotations to the pdf-file, but could be wrong. You might want to take a look at the Xournal port for the DR1000.
Another tip is the Mackx patch (which can be found in the developers subforum). It's adds very useful functionality to the overall device like keeping lists of last-read documents, menu customization and automatic opening of documents at startup.
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