Most window systems use a desktop metaphor. Part of this metaphor is the idea that windows are stacked in a notional third dimension perpendicular to the screen surface, and thus ordered from "highest" to "lowest". Where two windows overlap, the one higher up covers the one underneath. Even a window at the bottom of the stack can be seen if no other window overlaps it.
A window's place in this ordering is not fixed; in fact, users tend to change the order frequently. Raising a window means moving it "up", to the top of the stack. Lowering a window means moving it to the bottom of the stack. This motion is in the notional third dimension only, and does not change the position of the window on the screen.
You can raise and lower Emacs frame Windows with these functions:
nil, activation of the minibuffer raises the frame
that the minibuffer window is in.
You can also enable auto-raise (raising automatically when a frame is selected) or auto-lower (lowering automatically when it is deselected) for any frame using frame parameters. See section Window Frame Parameters.
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