Well, first the proper way to do child windows in a main windo is really to use sub panels. They are the LabVIEW native way of embedding VI front panels in other VI front panels and work across all LabVIEW platforms the same. Using Windows API calls, if you do that, is cumbersome, likely to cause all kinds of troubles if you do not know EXACTLY what you are doing and a maintenance nightmare as you will keep running into strange effects with new Windows versions sooner or later.
That said, whatever you do, LabVIEW subpanels or Windows parent-child windows, they are setup at runtime and you as the programmer are the sole responsible person to load them at the right time in the right plkace and with the right content. If you want to have an ability to rebuild a particular constallation of UI, you will have to program a way to save the current constellation into some config file and on reopening that constellation rebuilding that from the config file.