How do I control what the contents of http.include is for each domain?

I know that I can use vhost.conf to manually make changes on a per domain basis, but that doesn't help me when I want to apply stuff across hundreds of domains.

I know I can use /etc/httpd/conf/http.conf to make global changes, but those won't be reflective on a indevidual domain level.

For instance, how do I change the include path for every domain on the server to reflect a path within it's own directory structure?

Thanks