Subapplication pop-up: Get main application window to appear over pop-up sub-app

I have a pop-up window that you can drag around by the header. My main application window you can also drag around by the header. I want the main application to appear above the pop-up when it's selected, and vice-versa when the pop-up is selected. However, it seems sub-applications are designed to always be on-top of their parent application.

Window Control Object - Bring window to front doesn't seem to have any effect. Any ideas?