I demo The Bad Wrap templates at many of the tradeshows for SAi. It really is a pice of cake. In short:
1. Drag and drop any background or logo images into the green layer group (design). You can move the layers around, just be sure that they stay inside the green layer group. You can also manipluate any othe elements in the green group using Photoshop tehcniques, again, just be sure that they stay in the green group.
2. After you have your design down, you can hide the "template group" (red, I think) and your full print design should be visible without the vehicle now.
3. At this point you can simply save the design as a flattened tiff and send it to your RIP to cut up and print (over simplified). Yes, you will need to print it at 1000% as it is at 1/10th scale.
TIP: Before hiding the tempalte group, I like to cut up the pieces in Photoshop so that I have the benefit of choosing where my seems go. For example, I use the selection tool and select a rectangle area around the drivers door (leaving a couple inches around the door so that I have enough print to work with while installing. After making my selection, I turn off the design layer and use Ctrl-Shift-C to merge all the layers in my selection and copy them to the clipboard. From there I create a new file (the clipboard's dimensions should be automatic) and paste my selection. Now I have a flattened file for my driver side door to send to my RIP. I like to save the individual files in case I need them for printing later (installation mistakes or if the driver has an accident and I need to replace a specific area of the wrap). This TIP isn't exclusive to these templates and can work with any Photoshop files that it might be relevant to.
P.S. Please let me know if you have any questions that I might be able to help you with regarding the templates. While I am not employed by SAi, I do have a pretty good idea of how they work.