At the moment there is no way to do that automatically, because CustomBuild is only able to install 2 different versions of PHP (not 3 as you mentioned).
I would use the PHP SELECT VERSION (http://www.outservices.net/phpvs.php) to select version of php for my domains. But if I setting version of php to php4, the phpinfo () I have another php5. How can I resolv the problem?
in phpinfo() (for test I have set php4 to default php version for a domain) the configurations file path (php.ini) is set to: /usr/local/etc/php5/cgi/php.ini and all parameters are set with settings from that file and not with those of the files in / usr/local/etc/php4/cgi/php.ini