I'm going to assume two things:
- If you have successfully installed koreader, then you've also configured nickel to ignore hidden folders.
- These libraries have no need to interact with or be aware of one another.
I use koreader exclusively for pdfs and cbzs which I don't want nickel to index (because it just clutters the library and I'll never use nickel to view them). So I put those files in a hidden folder called
.misc (the dot is important) and set my koreader home folder to it (long press on the folder, I believe). That way, when I boot up koreader, it opens to that folder, organized the way I want it to be.
You could probably do something similar.