How does a CPU work?
A detailed answer is not so much a company secret, but rather the subject of several semesters at a University.  Don't expect to get a complete answer here.  

One of the best books on the topic is this one:  http://www.amazon.com/Computer-Architecture-Fifth-Quantitative-Approach/dp/012383872X/ref=ntt_at_ep_dpt_1

There are also numerous books on digital logic design that would be good to read as well.