I have a Wordpress multisite subfolder instance that I would like to track via Google Analytics.

I guess optimally this would be a plugin which I could track each site in two places

1. The Main Tracking Code which totals all traffic from the Multisite instance
2. The Individual Site tracking code to see how each site specifically is doing.

I think this plugin would have worked for me if I had a subdomain multisite instance:

http://wordpress.org/extend/plugins/google-analytics-multisite-async/installation/

I know I can manually place the dual tracking code (http://www.markinns.com/articles/full/adding_two_google_analytics_accounts_to_one_page) but that would involve editing a theme and I have multiple sites using TwentyEleven template. I don't think I can edit the theme and not have it wreak havoc on the rest of the sites using TwentyEleven.

So has anyone done this? Is there a a technique I'm missing? Is there a plugin available to do this in Multisite Subfolder installations? Is there a way to manually insert GA codes into themes which are used by multiple sites?

Any insight is appreciated.