In case anyone wants to know, this is my go-to recommendation for "getting started": http://www.lrde.epita.fr/~adl/autotools.html . Extremely thorough, and shows how all the different pieces work together. I'd read it anyway, even though you've got started. It's very, very good.

I've also found Diego Pettenò's "Autotools Mythbuster" to be quite good: http://www.flameeyes.eu/autotools-mythbuster/index.html . His old article "Best practices with autotools" isn't bad, but a little light: http://www.linux.com/archive/articles/114061

You may also want to browse the autoconf and automake tags of Diego's blog: http://blog.flameeyes.eu/tag/autoconf and http://blog.flameeyes.eu/tag/automake

A thorough reading of the autoconf and automake manuals also points out common pitfalls.