The S12 series of embedded controllers have their documentation divided into specific modules (ATD, SPI, SCI, ect). This is a departure from the old HC11 "pink book" that had everything in one concise location. I counted 17 different documents associated with the S12 controller (that I've located), this is in addition to the documentation provided by the chip integrator (Elmicro & Technological Arts are two companies that integrate the CPU with all supporting electronics on a single board). If you haven't purchased a demo board, I would highly recommend it. You usually get everything needed to get up and running so that you can get your feet wet a little at a time.
Two examples of Freescale documents are the: MC9S12CFAMPB document & S12SCIV2 document. I think if you look under the specifc part, there should be a list of all documents.
Good luck & happy coding.
