If you encounter a pop-up on a site, the window that appears here is seen as a windows application and acts as if it is not part of chrome. Therefore, you need to find the name of that window from wispy and pretend to open that window with Applications - Open. Thus, you are connected to that window. Then you can click where you want to click.
Important note: Since it is seen as a window, you can easily find its XPath with the help of wispy.