Well, In windowmaker I never edit the config files by hand, unless I want to do some serious tweaking for themes.
Usually changing the menu just involves firing up wprefs, going to the menu area, and draggins stuff around;
When you open wprefs, and go into the menu area, another menu appears,, this one is just for editing the real menu,, in other words, you make this 'edit menu' look like you want the 'real' menu to look like, so after you press 'save', the 'real' menu should look like what you made the 'edit' menu look like.
Ok, by 'dragging' I mean the following,
To delete something (submenu, program name), just drag in out of the 'edit' menu, and release the mouse button. And it disappears.
To add something (A button to run a program, or a submenu or whatever), just drag it from within wprefs to the 'edit' menu, and release the mouse button.
To Rename something, double click on its name, change it to what you want, and press enter.
In other words, just fiddle around.
Its actually quite intuitive.
Have Fun!
RefriedBean