Google Analytics Plugin with MultiSite

I have a MultiSite installation with over 6,000 sites and over 100 custom domains (currently using WPMU Domain Mapping plugin).

If I use the Google Analytics+ plugin, will it track all the custom domains so that I can view their individual stats?

I currently am using this Google Analytics plugin (http://wordpress.org/plugins/googleanalytics/). In order to view the custom domains, I have to set up unique views in my GA account and then filters. However, GA limits you to 50 views.

Thank you for your help!