Add analytics to one blog in header and footer

I'm a total newb on this one.

I have a question about adding analytics and webmaster tools to the php files in one or more blog. However from this thread: https://premium.wpmudev.org/forums/topic/how-to-customise-a-theme#post-10968 I get the impression that I can't assign the codes to each blog exclusively in the WPMU set-up.

Do I just add the codes to all my used themes and then each report will be discernible by blog, as in no need for them to set up analytics codes for each site?

Let me know if that makes sense.

Thanks

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