You could simply do "touch /etc/puppet/manifest/site.pp". The file must be readable by the puppetmaster process (so you might need to twiddle ownership or permissions), but there is no specific required content.
As you are just starting to play with Puppet, the first (and maybe the only) thing you are likely to want to put in your site.pp is one or more node declarations. Again, there is no specific content required for those -- the whole point is that's were you declare what
you want Puppet to manage on the target node(s).
Overall, I would recommend that you read the "The Puppet Language" section of the Puppet language reference (
http://docs.puppetlabs.com/puppet/3/reference/index.html), and at least skim the "Generated References"/"Resource Types" section.
John