It's more than a philosophical question. You have only one user interface. It can have any number of panels, but together they make up the one user interface.
Since you have only one user interface, you should run it only once. It is typical to RunUserInterface in main(). If you start a project by creating the UIR file and then goto Code >> Generate >> All Code, you'll see the structure that CVI creates.
Another option is not to use RunUserInterface at all, but call GetUserEvent in a loop. See the GetUserEvent.prj sample project that ships with CVI.