You can now use WPrefs.app ( its appicon looks like a heart rate meter with a GNUStep icon backgroud ). Note that this will replace any oldstyle menus and there is no way to convert the oldstyle menu to the new libproplist style menu.
For old style menus, edit the file
~/GNUstep/Library/WindowMaker/menu
and save your changes. Window Maker should detect the change and automatically update. If you are having a problem getting it to reload the menu, try