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Well, first, you need to be an admin on the wiki in order to edit the navigation. Then, you need to go to MediaWiki:Wiki-navigation to edit it. (The "contribute" button in the upper-right corner should have a link that will take you to that page so that you can edit the navigation.) When you edit the navigation, you use asterisks for each "level" in the navigation menu.
*This is a level 1 option
**This is a level 2 option
***This is a level 3 option
And the syntax for each menu option goes like this:
^This very line of code makes a navigation link to Blog:Wikia_Staff_Blog with text that displays "Staff Blog" in the navigation bar at the top of your screen right now. Notice that this syntax is similar to how you create a regular wiki link, i.e. [[Blog:Wikia_Staff_Blog|Staff Blog]] makes Staff Blog.
Some wikis (such as Community Central here) use what's called "Expanded Wiki Navigation" -- it's a feature that admins can enable at Special:WikiFeatures. Basically it makes the navigation bigger, styled differently, and raises the maximum number of links you can have.
A good way to learn how to edit wiki navigation is to look at the wiki navigation of another wiki and copy the pattern you see there. Take a look at http://community.wikia.com/wiki/MediaWiki:Wiki-navigation and try to copy the patterns you see there when editing your wiki navigation.