TTmotors:
CATIA V5 has a fully parametric application for 3D tubing layout. Strangely enough, it's called "Tubing Design".
You can also layout your header using any CAD system by using curves and points along the tube centerlines. It's the length of the various tube sections that you should be concerned about, so a crude layout of lines and curves should work OK.
Most header designs I've seen are initially mocked-up by hand using "J" and "U" bends. It gets dyno tested, and if it proves satisfactory, a jig (and maybe a drawing) are produced from the prototype. I know it sounds a little un-scientific, but header design is still somewhat of a black art.
Regards,
Terry