First of all you might want to explain what you mean by "apply model to entire site". A model in Alfresco terms is a dictionary model of allowed types, aspects properties etc. and is always available globally within a tenant (if you don't use multi-tenancy, you still have a "system tenant" in which you work from a conceptual perspective).
If I understand, you can apply rule on the root directory of a site, navigating via repository.
Browse Sites > yoursite, and apply your rule (to apply a custom type for every document on creation for example) in documentLibrary folder. Once rule is created, you can even run it as an action from rule management, on the previoulsy created contents of a site.