As Unseen said its just practice, trial and error.
For starters take a look at this
guide by Jaz, this shows what percent each logo/shape needs to be scaled for each panel you may still need to tweak the logo if wraps around a curved surface like near bumper corners, wheel arches etc.
The only way to line them up is position your first logo then save the skin and load it into the cmx viewer (as you did for the ss you posted) then if it isnt alligned correctley move the logo slightly re save and click reload in viewer then just keep repeating this until it is lined up correctly.
It can be very time consuming especially when you pick a skin like the one you have chosen with lots of logos that lap over panel edges. Try using the wireframe to get refrence points where the 2 edges meet this will at least give you a rough idea of were to place it.
Not sure how you sort your layers out but I ususally have a "decal" layer that is only used for the logo's, makes it a lot easier if you miss one that is out of place or not lined up and you need to cut it from the skin to reposition it.
Once you've got one or two lined up you will find it easier, just keep practicing, Good luck and keep us updated