I don't like the standard files in Nautilus (the ordering by data types - Images, Music, Videos, Documents etc.), how can I change this or can I change this ordering without getting problems with several software or Ubuntu one?
You might use
xdg-user-dirs to set up user directories.
Your directories are stored in
xdg-user-dirs man page is readable at http://www.unix.com/man-page/OpenSolaris/1/xdg-user-dir/