Embedded Linux Primer

Mark Kim as a nice beginners overview of Autotools. Worth the time to read it, if this is something that you're interested in!

http://markuskimius.wikidot.com/programming:tut:autotools

To summarize (overly simplistic view!)

autoscan --> creates initial configure.in (called configure.scan to avoid overwriting your pre-existing configure.in)
Note: you will have to edit at least AC_INIT and AC_OUTPUT in the configure.scan template that autoscan produces.

autoconf uses configure.ac to create configure