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You cannot simply put module in user menu.
You can remove module from main menu by giving it the order = 0 in modules admin.
If you want to make custom menus - it is worth trying MultiMenu module, check the xoops.org FAQ as well.
I might have missunderstood your post. Extra advice: go to the groups admin in admin panel. You can set which module is visable and accessible by specified groups. Many modules has got their own permission system, check it.