Well I might wright page or two tonight. I know it calls for some docs.
Every scale is per pixel, or it is mentioned in mini-help for actual parameter (or it should be). Also mouse can be used for reading results, it shows distance, depth, actual transmission loss and difference against simple spherical spreading.
This simulation has little actual sonar know-how. It's ray-bending based on propagation speed changes. This applies to sonar too, so if you enter correct values, you'll get more or less correct prediction for sonar, but it would be used for light propagation on atmosphere for example or anything similar.
As for books, this one is good, on the other hand the only I have:
http://www.amazon.com/Principles-Und.../dp/0932146627
MolonLabe: I'm not sure at all. Only only played with CZ for a while and I never actually used them in mission.