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How would I go about setting the up CNAME settings with my registrar to have multiple websites under one account ?

ex.

website1.com points to x website2.com points to y

Slightly unintuitively, you just set up a CNAME to accountname.pythonanywhere.com for all of them. This is enough to point the domains at the appropriate PythonAnywhere servers.

Next, when you create web apps from the PythonAnywhere "Web" tab, you specify the domain for each of them. This means that when a request comes in to our servers, we can route it through.