I have two Trek's, a Madone and a 1.2, and both bikes came with identical booklets and CD's and when it came to the nitty gritty they are of not much use. On most of the jobs in the manual it just recommends, take the bike to your dealer to repair etc. Oddly enough a few months ago I did find a more detailed Madone manual online, but dammed if I can find it on my PC now.
What I usually do though is just download the relevant things I need from the Shimano website for brakes, groupsets etc