TreeSurgeon is a tool that will set up a directory tree for you, with all the required dependencies and a skeleton nant file. At that link, you can also find a series of blog posts by its original creator, Mike Roberts, explaining some of the deliberate choices behind the structure that TreeSurgeon gives you, e.g. why it's OK to have duplication between lib and tools, why it's important to have all dependencies present etc.
I haven't used it in a while so can't remember if I still agree with all the choices it makes, but I don't think you can go far wrong with it.