Are you interested in the exhaust flow design or the physical layout design?
There is plenty books around on exhaust theory, I've generally used calculations from A. Graham Bell's books in Excel to get a "designed length" and then worked to keep close to that in steel by eye and tape measure. I generally don't get hung up on small differences in length.
If your developing a motor that runs over an extremely narrow rpm band only like a stationary motor or a vehicle with infinitely variable transmission it may warrant getting them spot on but in a real world vehicle I recon a slight tune spread is probably not a problem.
PipeMax used to be the standard other software was judged by, not sure if that is still the case.
Any CAD program should let you draw a path and extrude along it to visualise clashes.
Cheers
jon