I'm not sure I understand what your problem is - in general, there is a limit to the amount of attention a program can require a user to give it - you shouldn't let a user do multiple things at the same time. Preferably, each task should start and be finished.
That said, there are of course valid reasons for displaying several front panels at the same time. You can do so by arranging the windows so that they don't overlap or you can have them overlapping or you can use a subpanel control to display one front panel inside another.
If you call the subVI directly within the event structure, the loop in the main VI will not continue running until the subVI has finished running. If you want its front panel to close when it's done, right click on its icon and select VI Properties. Then, go to Window Appearance, select customize and set Show Front Panel When Called and Close Afterwards If Originally Closed to true.
If this doesn't help, write some more details about your problem.
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