KOReader and the stock software coexist on the Kobos and Kindles, both function without regard to the other. You can still do anything with the stock software, that you could before KOReader was added. Trying out having both for awhile, won't hurt anything. You can put books/pdfs that you don't want the stock software to deal with behind a "hidden" folder and the stock software won't even see them.
Luck;
Ken
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