In fact, you can add any UIView as a subtitle to CCDirector.sharedDirector().view at any time in a running Cocos2D application.
I bet the only reason you really have to mix Cocos2D and UIKit is to create menus and other user interfaces in UIKit and launch the game using Cocos2D. To do this, you can simply find the place where Cocos2D is initialized and replace it with your own UIKit stuff, and then anywhere you can run the Cocos2D scene using the code you replaced. If you want to make this method that you are looking for,
- (void) setupCocos2dWithOptions:(NSDictionary*)config
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