Educational resources that might help with understanding how ICs are constructed
EE760 VLSI CAD: http://www.ece.cmu.edu/%7Eee760
Focuses mostly on building layout + routing tools, good math basis too
Project2- Transistor Equivalent Checking: http://www.ece.cmu.edu/%7Eee760/760docs/PROJ2v1.pdf
Converting transistor-level netlists to check boolean logic
Reading The Silicon Zoo
Oaklahoma State University assorted VLSI links