How to configure analytics for Multisite with mapped domains (A record)

This is the first time I am trying out domain mapping and I want complete URLs to work for the networked sites. I followed the instructions for a name mapping, and it seems to be working, but now I want to add analytics. Google asks if I want to add analytics for a single domain, One domain with multiple subdomains, or Multiple top-level domains.

Do I choose subdomains even though they should show in browser as the url only?

Am I not understanding how domain mapping works? Any help is appreciated.