I use Calibre it's free and can sync the books between itself and the T1. I was using Calibre for a library before I even owned an ereader I think it's probably the best way to keep ebooks organised.
You also should know you should extract files from zips before running them it sounds to me like you might be trying to run it inside the zip and that will give you problems. Usually you can just right click on a zip file and choose extract here.
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