The ./configure script will analyze your environment and create custom Makefiles particular to your system. Aside from all the standard autoconf stuff, ./configure does the following:
You can manually specify the location of apxs by using the --with-apxs option, e.g.:
$ ./configure --with-apxs=/usr/local/apache/bin/apxs
$ ./configure --with-apache=../src/apache_1.3.12 --with-apxs=/usr/local/apache/bin/apxs
If the Python installation on your system is not suitable for mod_python (which can be the case if Python is compiled with thread support), you can specify an alternative location with the --with-python options. This option needs to point to the root directory of the Python source, e.g.:
$ ./configure --with-python=/usr/local/src/Python-2.0
Note that the directory needs to contain already configured and compiled Python. In other words, you must at least run ./configure and make.
Also note that while it is possible to point the --with-python to a version of Python different from the one installed in your standard $PATH, you will need to have that version of Python installed as well. This is because the path to the Python library, which is retrieved from the python binary is going to point to the place where Python would be ultimately installed, not the source deirectory. Generally, it's best to try to keep the version of Python that you use for mod_python the same as the one you use everywhere on the system.