If you are going to create set of pp files, as given in the documentation, it's suggested that you put them all together in a single directory (named "manifest" by convention) so that when you run the puppet "apply" command on the directory, puppet will parse all the pp files in alphabetical order and execute them all together
Ex: puppet apply /etc/.../puppet/manifests
For execution of a single file:
puppet apply /etc/.../puppet/manifests/JohnDoe.pp
Reference: http://docs.puppetlabs.com/puppet/latest/reference/dirs_manifest.html