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Marvin is a little confusing to get started with and especially getting your books to, since you have to select something from your connected iDevice. However, once you get it sorted, you will wonder why you ever bothered with iBooks. Getting books into Marvin is a snap after the initial learning curve -- it was simple to get my 4000+ book library on there. That would have been undoable with iTunes.
I'd suggest removing the iTunes plug-in. If things don't work out you can always reinstall it. Marvin's creator is active here on MR and if you have any problems and post in the Marvin forum he or someone else knowledgeable will help you.
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