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I have never used iRex's Windows software. You may need it to add notes from the iLiad to the original PDF, but I not sure even that is required.
Any desktop PC should see the iLiad as a USB filesystem. Unlike most other Readers, you only get one of the iLiad's filesystems at a time (internal, CF, etcetera), selectable via the setup menus, and only if the iLiad is displaying the contentlister when you connect. Just put your documents where ever you want, and feel free to create subdirectories (folders). When you open a PDF or ebook, the iLiad will move it into its own subdirectory and add a few files. This is its way of handling metadata (you don't see these files via the contentlister, but you will via USB) and is normal.
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