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 edublogs.com), and then we have (will have) a bunch of subordinate sites. So it'll look like:

main.com/site1
main.com/site2
main.com/site3

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

Can this be done? Hints on proper setup?

Thanks!