There are a few minor differences when using Google Sites under Google Apps. These differences are controlled by Google Apps Sites settings which can be found at:
(These are the key settings for those wanting to have their Google Sites in a Google Apps domain. There are many more settings which can be ignored by those only using Google Apps as a place for their Google Sites. More details can be found here http://support.google.com/a/bin/answer.py?hl=en&answer=55955)
Whether or not an account under a Google Apps domain can create a Google Site is controlled by the Site Creation option under the Org Settings tab at https://www.google.com/a/cpanel/..DOMAINNAME../CPanelHome#ServiceSettings/service=sites&subtab=0
Just below the Site Creation option is the default Site visibility option for other users within the domain
Sharing Options are under the General tab. These options control whether or not users within the domain can share Sites outside the domain and make them public or not.