Hi,
First, thanks for the beer! Much appreciated.
I'm afraid that with folder sites since it is really the same domain for all sub sites, from woopra's point of view it is all 1 site.
I'm not sure if woopra has any way to create segments for real time tracking, I know in google analytics there are ways of segmenting sites based on url segments so that you could have analytics reports for each segment. I can't tell you details how to do it as I'm not really a google analytics expert but I know enough about it that I'm sure it can be done. Maybe there is something similar in woopra. I just stopped using woopra because its out of beta and no longer free for sites that get a lot of traffic (I think 30,000 page views/month is all you can track for free but this site is pushing 200,000 per month).
Hope it helps,
Joe