You can set the SubVI to "Open Front Panel when Called" and "Close Afterward if Originally Closed" - that makes it a pop-up window. When your main calls it, the subVI window opens up. You do stuff, click the DONE button, and it disappears, and the main is up front again. (Make sure your subVI is MODAL if you do this).
You can use the VI SERVER to load the VI, given a path to it. You can set the subVI to "Open Front Panel when Loaded", or you can set FRONT PANEL.OPEN to TRUE when you want it to appear, and FALSE when you want it to go away.
You can make a subpanel on your main, and have the subVI inserted into that.