Give
KOReader a try, it uses a simple file manager, so you can use your existing file structure. Even if you decide that you want to use the calibre generated file structure, KOReader has several functions that work with calibre. Calibre is handy for preparing files for drag&dropping to my file structure on my device. I don't use Nickel or the Kobo readers anymore, but if you do, the KSM launcher program has a number of features that help with nickel.
Luck;
Ken