I think the quickest way of doing this is in Illustrator. If you have overlapping shapes you can get rid of the overlap by using the pathfinder-tool “trim” (Window – Pathfinder – “Trim”-button) when both shapes are selected. That creates a neat border between the shapes. (Obviously works only if the shapes are vectors and not pixel). If they are pixel, using clipping masks in Photoshop might be the quickest way.
Hope this helps.