Properly handling menu items in a custom module
You can programatically add/remove menu items on install/uninstall and/or enable/disable events. But that's not how we do usually. 

Implement hook_menu and you will be fine to go with almost any menu item implementation. 

A few points. 
Set menu router item's 'type' =&gt; MENU_NORMAL_ITEM and it will now be in a menu. Unless you set 'menu_name', it will be placed in the "navigation" menu. 
See the huge (and very helpful) text on the page. Also, have a look at examples module for high-quality hook_menu examples. 

Good luck!