I wasted a lot of energy on trying to change the menu. I take it that the tool you are describing is that which does not require the root password.
The conclusions I've reached are
1. The OS will not honour any alterations you make to the system menu. Move, remove and rearrange to your heart's content, sooner or later the system settings will prevail.
2. You can, however, add items to the menu. That applies at the system level as well as the user level.
3. Stupid things can happen. Because of the interaction of the files in your home /.menu folder, you end up with duplicates, triplicates, there seems no limit to the number of copies of system menu entries. That copying only seems to take effect at the user level.
4. The changes you make are contained in a file called added_by_menudrake in your /.menu folder. Edit that by all means and as soon as it is correct, copy it to a safe place. If that does not stop the duplication of entries, just delete (or move) the other files in that folder and do as follows.
5. In the menu editor, use the command File >Reload System Editor and save. That will refresh the system part of your menu and obliterate any changes you've made.
6. Now, copy your added_by_menudrake file back to /.menu, overwriting the empty file which has replaced it and use the command File >Reload User Config. Save. The menu is good to go.
I eventually simply added my own submenu, using my user name. The submenu has four branches: Sys, Internet, Start, Files. The submenu contains commands I frequently use. The last branch contains shortcuts to open specific files.
In KDE, I can have an icon for each branch on the top panel. When I click on the icon, a list of the commands in that branch drops down and one click opens the tool, application or file.
I ignore the rest of the menu except occasionally when I want to use something not in my personal submenu. And I stay sane. (At least, I believe so.)
