Configuring Domain Names (with "www" or without)

I have a Worpress MU set-up and have Domain Mapping installed. My question is…when I configure domain mapping for a domain name, if i configure the name without “www” prefix….when you type the domain name in a browser, it always automatically removes the “www.” Should I configure 2 separate domain names (mydomain.com and https://www.mydomain.com)? Will the search engines view this as duplicate content?

Thank you