It's pretty much up to you. There are a couple different approaches to take.
Either you could have another gui class and offload more functions from the main window into the popup one, or you could create something yourself to handle the instructions from the main window that wouldn't be as complicated or sophisticated as a new gui (for example, something that simply drew an image when told to, held its x & y, etc).
After doing either of those things, you could have the popup window be contained and controlled by the primary window, which would just involve having them as fields within that class and doing whatever needs to be done to them through that class.
Or you could keep the handling of the popup window external, doing things to it alongside the main window. That would leak a little more gui handling into the outside world though.