I haven't really used Make in any big projects (read: 100s of files and dependencies), but that's mainly because I have a habit of breaking components into smaller projects and thus keeping things, including my Makefiles, very simple. For project structures like that, I think your tools and book are overkill, so I'll recommend this reference from Oreilly's UNIX in a nutshell. I found that this is by far the most easily digestible reference for GNU Make I can find that's free. It's fairly to the point and concise as far as reference go, you can read the whole thing and have a fairly good understanding in under an hour. It's a reference that I go to 90% of the time, the other 10% come from Google and trial and error.
http://oreilly.com/linux/excerpts/9780596100292/gnu-make-uti...