Ecky,
I rescind my former statement, you are using the tool correctly. However the tool that you are using is using an older version of the Aerodynamic Streamlining Template. There is a newer version which is slightly more aggressive, the AST-II.
If you notice, your car (which is extremely low drag) doesn't fit the AST-I, but perfectly fits the AST-II.
I will find a link to the online version and post it here.
Edit:As promised, here are the links to the AST-II, and Aerohead's discussion about the differences between the two.
http://ecomodder.com/forum/372995-post533.html
http://ecomodder.com/forum/373016-post534.html