Getting into the physical meat of it is tough, since most of the tools we use (measurement microphones, high-quality AD/DAs, software, etc.) are expensive. The theory can be a bit more accessible – though like most things, it often doesn't click for people until they get a chance to do it themselves.
The industry standard textbook, were something like that to exist, would be Bob McCarthy's "Sound Systems: Design and Optimization: Modern Techniques and Tools for Sound System Design and Alignment." [1] It's dense, but a great read, and should be accessible for people with a decent knowledge of the concepts behind FFT and basic signal analysis.
If you're just looking to play around a bit, you could try downloading a demo of SMAART 7 [2] from Rational Acoustics. It's basically a soft dual-channel FFT analyzer. We use it to compare a generated signal (usually in the form of pink noise [3]) with a returned signal (a copy of that signal sent to a speaker and returned to the analyzer through a reference microphone.) By comparing these two signals, we learn basically all we need to about how sound is acting in a given space: we know it's latency; it's frequency response due to signal processing, the physical nature of the speaker cabinet, and air loss; and it's phase response due to the same. The difficult part of the process is interpreting that data and using it to make informed decisions about how and where to modify signals and speaker positions.
[1] http://www.amazon.com/Sound-Systems-Optimization-Techniques-...
[2] http://www.rationalacoustics.com/store/smaart.html
[3] http://en.wikipedia.org/wiki/Pink_noise