KOReader is an addon reader program that many find handles PDF documents much better than the stock Kobo or Kindle software. Once the
Kobo Start Menu is installed you can launch into the stock Kobo Nickel interface or KOReader or
Coolreader or Plato readers. With Tshering's KSM9 all you need to do to install KOReader & Sergey's Launcher (with his Coolreader port, as well as games and utilities) is to copy the "koreader" and the "vlasovsoft" folders into the .adds directory, that KSM creates. The folders are inside the download packages.
Both KOReader and Coolreader use a normal file browser and whatever file structure you wish. If you put the files you don't want to use in the stock readers into a "hidden" folder (a folder/directory that is named with a leading dot/period, like .PDFs or .books) they will not be processed into the stock database.
Luck;
Ken