I don't understand how deployment, source control and not patching your live code have anything to do with PHP.
Keep your source in a svn or git repo, export the new release branch or bug fix release to a testing box and once you're happy move it over to production. What does any of that have to do with PHP itself?
If you're talking about moving from one version of PHP to another, just compile the new version of php in a different directory from the old version (e.g. /var/lib/php/5.4 ), create a new virtual server definition in apache and point it to the newly compiled php version (e.g. using Apache's mod_fcgid) and test your site. Once you're happy, make that virtual server live to the public and retire the older one.
Keep your source in a svn or git repo, export the new release branch or bug fix release to a testing box and once you're happy move it over to production. What does any of that have to do with PHP itself?
If you're talking about moving from one version of PHP to another, just compile the new version of php in a different directory from the old version (e.g. /var/lib/php/5.4 ), create a new virtual server definition in apache and point it to the newly compiled php version (e.g. using Apache's mod_fcgid) and test your site. Once you're happy, make that virtual server live to the public and retire the older one.