You can add with very little effort under the box tab of CSS sculptor.
In your case, I would be tempted to add a new div within the header div section, and to do this, you simply click the head div and then click the + button. If it falls in the wrong place, you can move the added div up and down or even make it a child div or stand alone div using the buttons on the right.
A good starting point for what you have described would be to use the provided template of 2 column fixed with header and footer, and then construct your div bearing on mind the size of the flash file that will eventually be sitting within it.
