Kit,
The URL option you're using is one way to do it. Basically, for any comment boxes for a specific article, you'd need to make sure you include the same href to that article. That way, no matter what URL the user is actually on, the comment will be for the 'common' href you specify.
The other option is to use the JFBCContent plugin (configured in the "Social" configuration area of JFBConnect). There is a lot of code to try to make sure we generate the same URL for the same article regardless of whether its shown on the front-page, a blog view, or standalone. It's not foolproof in case you have multiple menu items pointing to the exact same article, which can create a new SEF URL for each instance. This is uncommon, however, but it happens. In general, the Content plugin has been refined over the last year to be very accurate in creating the same URL and is what we'd recommend instead of adding your own comment box to each article..
Although the module/tag method, when done right (using the same href per module), is guaranteed to always be right since you do it yourself, it can be much more tedious.
Hope that helps explain,
Alex