Yes, using popup is the right way, however unportable (popups act differently in linux - they can be just in foreground).
Mirek
Any plans to improve Popup or TopWindow behaviour?
Just to make it clear, in standard X11, you cannot have "decoration-less" window that would allow user to make other window active. This is X11 feature and there is little that can be done with it.
I will explore "XShape" extension (used by that FX function), perhaps that is the way...