You can set a window to float on top of another using the window -parent flag.
For example, if you want to float win1 on top of the Hypershade, set the Hypershade as the parent of win1 as follows:
window -parent "hyperShadePanel1Window" -title "win1"; showWindow();
The following is a generic example that creates two windows, and sets win1 as the parent of win2 so that the win2 floats on top of win1.
string $win1 = `window -title "win1"`; showWindow(); window -title "win2" -parent $win1; showWindow();