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Actually, I've posted a great many times that KOReader does nothing to limit your use of the Kobo stock software (Nickel). The two are both available. So it's not exactly a matter of "switching over", you can easily have some ebooks that you read with the stock software and others that you read with KOReader. You can even use some of the KOReader features like OPDS catalog support to provide ebooks for reading in Nickel. Despite the nature of some of the posting here, the two (and Sergey's Coolreader port) work well together, for the most part.
There is the issue of Nickel's use and dependence on an SQLite data base. Although not required, I think it only prudent to have files that I will be reading exclusively in other than Nickel, inside a "hidden folder structure" (Hidden from nickel's processing). If both were accessing the same file, it seems possible that Nickel or KOReader could do something to the file that the other has a problem with. There is no problem with having two copies of an ebook file, one in a hidden folder and another open to Nickel's processing. (Of course you will probably want to hide any ebook files from Nickel, that are in any of the many formats that Nickel can't handle. For instance I have a lot of .pdb ebooks.)
As to series sorting, if you use calibre to send books to your device KOReader can use a search&browse function for the metadata.calibre file with the calibre tags and series data associated with those books.
While you can continue to use both, there have been a number of users who ended up using one of the alternative readers and rarely using Nickel again.
Luck;
Ken
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