That depends,are you just replacing the individual pieces or do you have an entire start menu to cut up(the best way)
Once you have a whole start menu,your gonna slice it into the sections you want.User pane,Programs,Places More Programs and Logoff area.
Easiest way to slice a graphic is to make new image with all layers from the start menu merged.
ctrl a(select all),edit>copy merged>ctrl n(new document),ctrl v(paste)
Now you have a single layer...Use the select tool to select the User pane area of your image,right click and choose layer by cut.Repeat for all 5 sections and you have your pieces.(once cut you can turn on and off each section easily to copy to the image you opened from Skinstudio)
Image size of the original must be changed to the size of your new graphic first.