Do you mean within the menu the icons for the apps are not where you think they should be? if yes.
you got a go into the desktop file and redo them
example, open a desktop file and look here, then change it. find one that is where you what it to be then look at this line within the desktop file : Categories
Code:
/usr/share/applications
Categories=X-XFCE;Audio;Mixer;AudioVideo;
then find the ones you want in that Category and just add that to the desktop file, edit and save as root user.