Wordpress-mu is a platform with which you can allow people to create their own blog. Most installations are in the subdomain format, i.e. you have the main domain such as www.example.com and the other subdomain blogs such as blog01.example.com, blog02.example.com etc…
If you want to get the stats for all these blogs, you have to register all the blogs individually.
You can not only register the main domain and expect Google to provide you with all statistics relating to the subdomain blogs. You have to go through the verification process in your Google account. Each subdomain is an independant site and you have to prove that the are yours in order to see all statistics and apply on them all the Google tools in your account.
Note that verifying the blog is a step, different from the one of creating a sitemap for your sites.

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