There is a property on the popup window that will force the popup window to stay on top of the Main Window. In the Designer, click on your popup window in the Project Browser (not the Root Container). Go to the Property Editor and click the Layer property. The higher the Layer number, the more on top it will be. If your 'windows’ Layer properties are all set to 0, they are all going to share the same layer. They can go back and forth over each other. If you set the Layer number to 1, the popup window will always be on top. Save and Publish your project.
After you update the Client, you will see your popup window on top.
It is also possible for you to open and set a specific location where you want the Popup window to be located. In Designer, click on your Popup window and go to the Property Editor. Click on the Location property and set to X to 300 and Y to 300 pixels.
Go to your Main Window, double click Open Popup Button to open the Component Scripting dialog box. Uncheck ‘and Center’ so your popup window will automatically open up in that specific X and Y location setting.
Save and Publish your project. In your Client, click the update bar, and then click on the Open Popup button. The popup window will open at the X 300 and Y 300 location setting instead of opening in the center of the screen.