Red Hat Enterprise Linux 6 includes man pages for autoconf, automake, autoscan and most tools included in the Autotools suite. In addition, the Autotools community provides extensive documentation on autoconf and automake on the following websites:
The following is an online book describing the use of Autotools. Although the above online documentation is the recommended and most up to date information on Autotools, this book is a good alternative and introduction.
The Autotools Plug-in For Eclipse whitepaper also provides more detail on the Red Hat Enterprise Linux 6 release of the Autotools plug-in. This whitepaper also includes a "by example" case study to walk you through a typical use-case for the plug-in. Refer to the following link for more information: