[Autotools] Subdirectories in the source tree

Hi everybody!
I'm currently developing an application that I want to distribute now. I
want to package everything using the autotools, so that everybody only has
to download the tarball, run configure, make and make install.
I already got things working with some test source files located in the same
directory.
But the application that I developed has a bunch of subdirectories that all
belong to the same target. My directory structure looks like this:

+ main.cpp
+ src
  |-- exception (directory with source files)
  |-- handler   (directory with source files)
  |-- number    (directory with source files)
  |-- parser    (directory with source files)
  |-- (some .h and .cpp files)
+ tests
  |-- handler   (directory with source files)
  |-- nodes     (directory with source files)
  |-- number    (directory with source files)
  |-- (some .h and .cpp files)

All the files have to be compiled. Then, all the object files should be
linked together to create an executable. That's it. A simple project, whose
files are located in subdirectories.

For me, it seems as if the autotools don't support subdirectories (only if
every subdirectory represents another target). Is there a way to do the
stuff described above in an elegant way? I would be glad if somebody could
explain me how to do it, or send me a link with a similar project that has
the same directory structure.

I'm currently using:
Debian Sarge, Kernel 2.6.17.11, autoconf 2.59, automake 1.4-p6, libtool
1.5.6, aclocal 1.4-p6 and bash 3.1.14(1).

        Thanks in advance,
                Andi