I generally draw my SP at true size just for the sake of simplicity. The margins won't effect how wide or tall each image is. They only effect how the images stretch/tile.
The sizing is in the extra settings tab for each part. Top part width will determine how wide the entire panel will be. The top part height determines how high the top part only will be. The next important setting is the left hand side width setting. This determines how wide the entire left side (including the all programs section) will be. Ignore the height setting here because that is determined by how many items you have in your menu. Next is the bottom part. You only have to look at the height setting here because as I stated before, the width is already defined by the top part.
Ignore the all program height and width settings. The width is already set from the left side and the height is hard coded at 30 pixels (keep the 30 px when you design your SP in mind).
You can totally ignore the settings for the right hand side. The width is determined by how wide the top part is, minus how wide the left part is. Height is also "user defined" by how many items are displayed on the SP.
Hope this helps