php install and setup questions

Hello, Installing,setup and configuring PHP to run on a Freebsd 4.3 machine. I am new to all of this. I bought enough books on all of them plus apache and mysql to wipe out 10 acres of rain forest. I have started but have overwhelemed myself. I have installed apache 1.3.19, freebsd 4.3, mysql 3.23 and php 4.0.6 (or whatever the latest is from the freebsd ports collection). When I installed the apache it also mod's for php3 and php4. Is that okay ? I have in my /usr/local/etc ini files for php3 (php3.ini) and php.ini (which I understand is for php4). There is also a directory under that ith a php.standalone with a php.ini So Which is the one to edit ? I would like to make sure I have or will be setting up a secure box so I am open to suggestions on how to secure PHP and of cousre any other advice on running PHP. THanks Kindly Md