I use the autoconf stuff only for libraries which have no other build solutions. So while I have some familiarity with the abilities, syntax and how they work I'm far from an expert. The primary reason I have never dug into them is that they are virtually useless on Windows which is unfortunately still my primary working environment. Using cygwin, msys etc to supply the tools is just not a very useful option when working in VC for most purposes. So, when I run into libraries such as those, I usually wrap them with CMake to do the actual build and call the './configure' from CMake on the platforms where it is required. For instance, GLog is my logging library of choice and on OsX/Linux it uses './configure', so I detect if the 'config.hpp' has been generated on those platforms, if not I call the './configure' to prepare the code but then compile the files through CMake, the reason being that I want the libraries embedded in my code and don't want to have to rely on pre-built versions which may have compiler flag differences and other such problems.
With all that said, if there is a specific problem you are having, ask away. I'm not very good with those tools but can often muddle through figuring them out..