The error “VBoxManage wasn’t found” is a bug of all IntelliJ products, not only PHPStorm, but also PyCharm, RubyMine. There is a workaround found on the stackoverflow, that helped me on OSX:

sudo ln -s /usr/local/bin/VBoxManage /usr/bin/VBoxManage

(http://stackoverflow.com/questions/31395112/error-setting-up-vagrant-with-virtualbox-in-pycharm-under-os-x-10-10)