Google Search Console (formerly Webmaster Tools) wants me to add all the domains I have for one site. Does this mean I should add www.site.com, site.com, and site.myshopify.com? If so, do need to set up sitemap, country, users, etc. for each of those properties? What is the best thing to do from an SEO perspective?
I'm Alex, your friendly neighbourhood Guru at Shopify.
In the case of Shopify, since your subdomains are likely just funneling into what you've set as your primary domain, you don't need to add all of your subdomains to webmaster tools as you'll be effectively tracking the same site. You'd be adding subdomains if you wanted to track each subdomain's site and sitemap separately, whereas in your case each of your subdomains share the same site and sitemap.
You don't need to set up a sitemap, as one is already created and managed automatically for you: https://docs.shopify.com/support/settings/general/where-is-my-sitemap-located
The same applies to Country, users, etc.
I hope that helps! All the best.