They are two specifications (or rather, conventions) that define the interface to the window manager. You need to read them to know how to get the window manager to properly treat your window:
http://tronche.com/gui/x/icccm/ ICCCM - the 'old' or basic specs
http://standards.freedesktop.org/wm-...ec-latest.html - EWMH, a extention to deal with more modern issues (yours is probably in this one)
As for transparency, I think EWMH has something about it, but in the end, its up to the compositing manager to determine how your window is drawn, so you cannot count on transparency.