I personally haven't tried or even attempted embedding Kobold2D in a UIKit app. It just wasn't one of my goals. Right now I can't think of a way that would be straightforward. In any case it'll be easier to move the existing source code and resources into a Kobold2D project, rather than attempting to attach the Kobold2D-Libraries project to an existing project.
Kobold2D runs quite a bit of setup code in main() and app delegate (KKAppDelegate). By the time the app delegate finishes, cocos2d is already set up and running.
You could try stopping the director for the time being, attaching your UIKit views to the already existing window, and later attach the cocos2d view to your game view controller when it needs to be displayed (and also resume the director). Something along that line could work, as long as the cocos2d view is never released.
I would also generally recommend not to re-create the cocos2d view anyway, since it's a costly operation and seems to be very untested. Issues related to re-creating the cocos2d view multiple times are common.