Even when selecting nginx - varnish - apache - php on "Select Webserver", Varnish is by default not enabled on domains. Which is good, because like you said, it is tricky.
I have experienced it to be extremely aggressive and will probably conflict with other caching tools.
To enable varnish, re-select the "nginx - varnish - apache - php" on "Webserver Domain Conf" for that specific domain.
Tip: To clear varnish cache for a user instead of the entire server, login to userCP and find the clear cache page.