You can try to temporary move yor top-panel away.
Then open all the debugging windows that are below it and move the top-panel back.
When C::B closes it should save the position of the windows.
Alternatively you can try to chose "always on top" (or something like this) from the menu you get with alt+right click or alt+space or whatever (depending on the windows manager you use).
On my debian system with lxde and openbox it brings the window in front of the panel.