Thank you all for your replies. I actually DO feel better
Guess I'm so used to the map structure in Windows I have difficulties using the (by me) dreaded search in the Kobo. What doesn't help in that is, I read a lot of "light novels", the japanese manga-related short books. Problem with these is, it's often hard to remember the author (for example, Tsuyoshi Fujitaka - My Big Sister Lives in a Fantasy World series) so browsing would make things easier for me.
As mentioned above, it's true that it would be easiest to put just the book(s) on you are reading right now and keep the rest on the computer. However, I like reading several books at the same time without plugging the Kobo into my computer to add books too often as well as just having a "library at hand".
Personally I would absolutely prefer browsing folders named by author - series but I guess I'm out of luck
I'll start reading up on how to hack/tweak the software, perhaps there's a setting somewhere that enables me to remove the things I don't need (like store, new books etc) to make room for a bigger "reading" category..
ps: yes, I changed the metadata using Calibre, deleted the old copies from the Kobo and exported the new ones but the author is still showing wrong. And only on one of six books in the series.. Even though in the filename AND the metadata in Calibre it's all the same