Aside from all the missing information, the way you can put a "pop-up" in a web page via javaScript is to create a hidden
of the desired size, and including the desired controls if appropriate. Since it's a already part of the page, and not a real pop-up window, it will not be blocked.
You use the DOM to change its visibility from 'hidden' to 'visible' (and back).
Use the z-index property to force it on top.
The size of your whatever can be gotten via javaScript, as well, assuming you know how to identify it, or, if it's the entire window, ask for that.