Automake will automatically copy over any Make targets you specify in Makefile.am into the generated Makefile. So you can generate any custom, complicated things just by including it in the .am file.
However, you shouldn't do this for everything -- that defeats the benefit that Automake is trying to provide you. Specifying
bin_PROGRAMS=foo
AM_CFLAGS=$(DEPS_CFLAGS)
foo_SOURCES=file1.cpp file2.cpp
foo_LDADD=$(DEPS_LIBS)
will generate a standard Make target anyway. I recommend you learn to use Automake macros for most standard things -- it will be more portable that way.
The best way to learn the rich variety of Autotools features is not to read the manual -- it's way too complicated and unorganizable. My suggestion is simply to take an existing open-source GNU project that is similar in build style (dependencies, platforms, etc) to yours, and examine its Autoconf and Automake files. The established projects have learned quite a few tricks that you can learn from.