Say you need to add a logo to the side of the car. On the Master Skinnerz pro-kit, find the appropriate layer for that relevant side. We'll call the layer "Left".
Click the layer name, "left", to select that layer. Press Ctrl+Shift+N to create a new (transparent) layer - this will be created directly on top of the "left" layer. Name the layer "left-side logos" or something that you can easily recognize.
Now open up the logo that you need on another window. To make it easier to explain, lets say only the logo shows up on that file/window. An image that dont need to be trimmed to get to the logo, something simple like this:
On the mobil 1 image, hit Ctrl+C (or use Edit>Copy) to copy the whole image.
Now go back to your prokit and click the layer we named "left-side logos". Press Ctrl+v to paste it. Even though you pasted it, it still remains sort of floating (if you look at the layers list - it'll show the image as floating layer (or something similar).
Move the logo around, resize it, rotate it - do whatever till you're happy with the oritentation and size. Once you're done, right click on the logo and select - (aah I cant remember the term, and I dont have Gimp atm...) something which means flatten or merge down (I think). What this does is it attaches the logo on to the "left-side logos" layer. The floating layer is no more - it's now intergrated into the "left-side logos".
Find another logo, copy, paste on to left-side logos. Move, resize, rotate and merge down (or flatten or whatever that term GIMP uses).
If all these layers sound too complicated, start off making rough skins. Open up the default skin and paint over it. There will only the default skin layer (background). When you paste a logo and merge it, it'll be fixed on to the painted body. If you need to edit the logo or the paint later, it would be almost impossible, but I think you better start of with a few crude skins till you get the hang of Gimp...