I have been learning C++ in school to create small command-line programs.
However, I have only built my projects with IDEs, including VS08 and QtCreator.
I under
This is what has helped me to learn the autoconf, automake, ...:
http://www.bioinf.uni-freiburg.de/~mmann/HowTo/automake.html
It is a nice tutorial progresses from a simple helloworld to more advanced structures with libraries etc.