Drupal 7: best practices to override a menu?

I have a menu defined in Drupal 7. Let's call it "top". This menu is already placed on the region that i want.

The difference is that it will show up as a select element in my drupal theme.

What are the best practices to override this menu?

Other menus will continue to show up normally, i only need to override this one.

Thanks!

Did you try using hook_menu_alter()?

You should be more specific, as I'm not sure what you actually want to change.