I use wifi and copy books from a share on a NAS. Calibre has no way to know what reader software you are using so you have to decide what format to use. I tag books I want on my Xoom and then write them in epub format to disc where I can get at them via wifi. Copy them over. Then I do an import in Mantano reader. Not perfect, but easy enough. I keep a few hundred books on the device. Add new ones now and then and remove older.
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