How do I set up Webmaster Tools for a Multisite Install

I have a multisite WP install set up as an events directory. As well as the parent site, there are 7 child sites of various topics. All of the events on the child sites appear on the parent site, however, the canonical URL for an event points to one of the child sites.

I don’t fully understand how it works, but all the data I believe is stored in the one database on the parent URL.

How do I put the Webmaster Tools code into the child sites, and how do I get webmaster tools to realise that the canonical URLs for each child site is the SEO info I am looking to analyse?