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.