Changing permalinks messes theme up

Could you explain what you mean by “it removes the theme”?

Could you also switch to another theme (e.g. twentytwelve) and see if that theme behaves in the same way?

Removes my formatting and css that I inserted into the header and footer

How its suppose to look

How it looks when I change to permalinks

If you link directly to your image from your blogpost or something then it should show up as you mentioned.

Permalink changes will support your post/page url. I’m not sure it’ll support media too.

Has nothing to do with the images it removes the formatting for the menu and footer

Here’s a whole page view

Screwed Up
Correct

This looks like some misplaced closing </div>s to me. A bit like when people forget to put code in backticks on the forum and the whole layout gets screwed up.

Could you say what exactly you are doing to “change [your] permalinks to reference the title from the default page number”?

Can you confirm that the problem happens in the Customizr parent theme with all plugins deactivated?