see documentation here: http://developers.facebook.com/docs/reference/fql/
the table you should request is here:
http://developers.facebook.com/docs/reference/fql/comment/
(this is also one of the first examples)
the key is that you can specify an identifier for each comment plugin you add. using this identifier, you can select comments using the api chart.
with respect to search engines, you should not give the impression that you are using different content for spiders than for users, so it would probably be nice to load comments by default api (please cache them), and then replace it with javascript, if javascript is available, so users can post new comments.
even better (in my opinion) will always display comments in html on your site and only load the facebook comment plugin if the user wants to make a new comment. but this probably requires another step for the user.
you can also read ajax chrawling diagram
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