Google analytics on subdir sites?

I've been looking at the Google Analytics plugin and realized I didn't know how to get GA to work with subdir sites. For example, we have a main site (think, like, and then we have (will have) a bunch of subordinate sites. So it'll look like:

We want to get separate analytics for each of site1, site2, and site3.

Can this be done? Hints on proper setup?