Makefile.am in the top directory should have the subdirs where Makefiles need to be created.
e.g Makefile.am for toplevel
+++++
SUBDIRS = src
+++++
and in the directory "src" you can possibly have the following Makefile.am
++++++++++++++++
bin_PROGRAMS = hello
hello_SOURCES = hello.cpp
++++++++++++++++++
Next you need to have a configure.in in your toplevel directory
following is just a template , read and understand on your own , i have no explanations
++++++++++++++++++
AC_INIT(src/hello.cpp)
AM_CONFIG_HEADER(config.h)
AM_INIT_AUTOMAKE(hello, 0.1)
AC_PROG_CXX
AC_PROG_INSTALL
AC_OUTPUT(Makefile src/Makefile)
++++++++++++++++
you are pretty much done with the files at this stage ,
$aclocal
$autoconf
$touch AUTHORS NEWS README ChangeLog
$autoheader
$automake --add-missing
