When using MPlayer in this way, I think the best option would be to create a second window.
Here are some ways you could take from here: a method that may not work on some versions / configurations of Xorg is to have the second window be the same size as the first and place it directly on top of the other (<with mechanism move another window when moving) and make the window transparent, except for your controls (transparency is a problem with some versions of X, check out some examples of this example at labs.trolltech.com).
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