Correct way to use hook_menu_alter
If two modules are altering the same menu item / form / page etc, last one will "win". 

If you need some control over this, and are expecting collisions, you need to implement hook_module_implements_alter:


  This hook is invoked during module_implements(). A module may implement this hook in order to reorder the implementing modules, which are otherwise ordered by the module's system weight.


Do your best to have your hook fire last, and if menu item you are altering does not look like the one you are expecting (it was altered already), write a warning message to watchdog.