Hi Justin,
right, the file is generated after running “up” the first time, but you’ll get the chance to edit it before the VM is actually built the first time. If you want to see the templates where it gets generated from, look in puphpet/templates/allinone and puphpet/templates/modman
Changes to php.ini configuration can be easily done in the config.yaml file.
In the modman/composer setup, you’ll specify the Magento version in composer.json. The important bit there is the download link to a tar.gz archive, usually from magentocommerce.com
In the allinone setup, look into puphpet/files/exec-once/70-install-magento.sh and change this line: https://github.com/schmengler/magento-boilerplate/blob/master/puphpet/templates/allinone/to-copy/puphpet/files/exec-once/70-install-magento.sh#L6