You can set the Main Interface
on the Summary tab of your target application.
See this image:

EDIT: Or, as Alan wrote, you can install it in your info.plist file.
EDIT 2: A. I understand what the problem is. You can use MainWindow as the main .xib file, but you need to edit which .xib is loaded in MainWindow. Open MainWindow.xib and select the view controller that is used. If I'm right, his class is set to A
If you want to use B.xib, you must change the class to B
You will also need to set the NIB for the view controller in the Attributes Inspector.
Define the class for the UIViewController, which is used in MainWindow.xib:

Install NIB:

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