Matt,
Glad you're enjoying JFBConnect! No problem for the question, I don't think that's specifically been asked, and frankly, you subscribed.. ask it again if you can't find the answer quickly
As to your question, yes, you can use different JFBCFan or Live Stream modules on each page pointing to different web-pages. There's a few ways to accomplish this, and you'll have to decide which works best for you depending on how you will know the proper URL from Facebook to point too:
1) Use the JFBCFan or JFBCLiveStream modules and configure them to only show on the menu items you want to. Create a new module for each menu item, and within each module, set the parameters for that specific sub-site area.
2) Use the {JFBCFan href=http://ww.facebook.com/your-page} or {JFBCLiveStream} tags within the content of each minisite.
The LiveStream module is simply a way to have a 'quick' discussion on your site. It really doesn't have to do with a Facebook Page, just so you know. The JFBCFan module can show the stream from your Page though.
Hope that helps, but if I just confused you more, let me know, and I'll gladly help explain!
Thanks,
Alex