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1. The Local calibre catalog is the one that you can edit, by a long press. The other supplied ones were also at one time, IIRC. Any change won't take effect until Koreader is restarted. Long press the Custom DPI and you should be able to set anything in the greyed out number range. A restart is needed here as well.
Setting the "Home directory" sets where the File Manager should open, on the start of Koreader. The ../ is to the level before the one you found it on.
Calibre has to be told where to put the books it sends to your device, or it will use defaults. If you are using the Calibre Server and Koreader's Local calibre catalog OPDS option, then you are offered a chance to set the download directory, when you download a file/book. To set the download directory you just long press on it and confirm the selection.
Luck;
Ken
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