ios-Unity always run, stop or remove UIWindow?

I am developing a native iOS app and I added unity (classes, libraries...). I have to use Unity only in some controllers. My problem is that I need start unity, later present unity view and when user tapped back button, the app will return to my native controllers. I have read that unity is always running in background and the only way is handle the UIWindows (set hidden true or false), but I think that should be a better way to do that. Any ideas? Thanks for your time.