Good sound is art. You get good sound through using all of your tools—experience, research, musical sensibilities, gifts, knacks, tests, measures... the most important of all your brain and your ears, listening with your primal and your conscience. Once you have a formula for your art and design you can mass produce it, using science to make it repeatable, to ensure consistency, to ensure quality.
But as to engineering good sound.... Every single great book on the science of sound: Helmholtz, Rayleigh, Jeans, Olson, Kinsler... "the ear is the final arbiter of tone" and who am I to argue with the Greats, and those that do generally do nothing but reveal their ignorance. Science is the passion of the material, theory through moments of insight or accident, chased with its process and expressed through math. Art is the passion of sensation, realized through doing, the seat of your pants, and expressed in, and received through, a kind of humanized transcendence. The value ascribed by mankind to sound and music is, and has always been, subjective. And I for one hope it aways will be.
The nudge for the above? Steve Guttenberg's latest CNET post "Can sound quality be measured?". I love Steve's think about it writing style, and I enjoyed the article, and his reader's comments.
One of the greatest album covers ever used to express the relationship of the music and science, PInk Floyd
The Dark Side of the Moon
—even if just one of the layers—and the music is pretty amazing too... in my case life altering. But that's another story.