Detecting hardware overlap
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Overlay surfaces are not associated with any system window, in principle they are surfaces that must be "composited" using the video framebuffer (or the main display surface). What you may find (depending on your API) if the hardware supports overlays, how many aircraft, supported formats (YUV, etc.) and so on. This can be done, for example, from DX and OpenGL.
Many tasks performed in the past using an overlay can now be accomplished with compositing support for modern window managers such as compiz, DWM on Vista, Quartz on OSX. In fact, I think that programming with raw overlay surfaces is discouraged as WM servers provide such opportunities for application developers.
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