*scratches head*
Sorry i'd love to help but don't quite understand.....
Your having trouble with a skin thats already finished?
or
Your making a skin and are wondering how people line up the roof bonnet side or whatever with whatever design?
Paint the sides first ... then estimate where the stripe will be in the top down section. Load it into the CMX viewer ... then make corrections until it's correct. The wire frame layer helps you estimate better.
Make sure you grab the skin kit first though. It has each part of the car separated into different layers. Can be found here: http://www.master-skinnerz.com/