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KOReader starts in its File Manager with it defaulting to "/mnt/onboard". You probably need to navigate to wherever your book files are located. The "../" takes you backwards in the file structure. "mnt/sd" is your external uSD card. Once you have the folder you want to start File Manager in, you can long press on it to get an option to set it as your File Manager home page.
For instance I have my ebook library at "/mnt/sd/.Koreader/Books" (the ".Koreader" directory is "Hidden" in that the stock Kobo processing will not see the folders and files that are placed inside it).
Luck;
Ken
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