If you use a clipping mask for each panel, it basically means everything in the panel stays in the panel. To do this trick, make the panels as white space in seperate layers, and use a stroke on each layer for panel borders. Then when you want to put a layer inside the panel, put them next to each other in the layers palette, point at the line between them and hold Alt. The cursor will change to a little pot thing. Then click to clip the upper layer inside the lower layer. Then it won't appear when outside the panel.
The most useful use for this is when you have big backgrounds and things bigger than the panel. Simply clip them to it and they fit perfectly!!!!