Board Thread:Support Requests - Designing Your Wiki/@comment-7981828-20130601153326/@comment-4674838-20130601165748

Generally speaking, you're not supposed to alter Wikia's interface according to Help:Customization policy and the Terms of Use. For the two items you mentioned: For either of these (or any additional) interface customization questions, you can check with staff at Special:Contact for a more definitive answer as to what's allowed and what's not, the above is just speculation on my part.
 * Wiki navigation bar &mdash; the "On the Wiki" menu is a key part of the Wikia interface, so changing its location or removing parts of it is not allowed. Other than that requirement, you are most likely free to do whatever you want with the navigation menu. For these "Mirror Universe" articles, if you wanted to have some sort of script that moves other parts of the navigation menu around or adds things to it, it should be okay.
 * If I understand correctly, you are suggesting that for "Mirror Universe" articles, you want to move the sidebar to the left and the content area to the right, e.g. like it is on Arabic language wikis (because they read right-to-left) &mdash; ar.wikia.com. The area of concern I think is that the right sidebar is a key part of the Wikia interface, and should display in its default location. Moving it the left with an interface customization script is most likely not allowed.