UPDATE: I solved it! This is how you load third party PHP extensions to the best of my knowledge.
I followed the instructions in the wiki to get my own php.ini file.
It worked great!
Now I'd like to use my local php.ini file to load up one of my own php extensions. I chose the Suhosin Hardened-PHP extension at http://www.hardened-php.net/suhosin/index.html
I ran the following commands:
> cd suhosin-0.9.16
> cp modules/suhosin.so /home/username/website/cgi-bin/
and I added the following line to the bottom of my php.ini update script:
echo 'extension="suhosin.so"' >> $INIFILE
I fired up a phpinfo page and I don't see suhosin loaded anywhere. I tried running ./php.cgi from a shell and see that suhosin gives the following error:
PHP Warning: PHP Startup: Unable to load dynamic library './suhosin.so' - ./suhosin.so: undefined symbol: OnUpdateInt in Unknown on line 0
I probably need to recompile Suhosin with different options. I'm getting somewhere! Woo!