Hi Olle, I don't think you can have two popup layers over one another,
I have not found this to be the case. I have a template I use to created artist's galleries for a site I maintain. This is one of the galleries. Each of the 8 thumbnails links to a separate pop-up layer and all the layers are one on top of the other. http://www.placitasartists.com/m_rackstraw/