Facebook makes it very easy to add comments to a website but with their old api and new api and updates its often difficult to follow what you should and shouldn't be doing. In the end the code was very simple but it took us a few rounds to get it correct. Bluetube interactive implemented facebook comments for one of our clients Ticket Alternative as follows :
Setup your commenting "app"
First you need to create an app for your comments and if you have multiple websites I'd suggest creating an app with a unique name.. You do this under "my apps" in your facebook account, you can read more about it
here.
You should now have an app id, and you'll want to cut/paste this somewhere for easy retrieval, it will look something like :
204151772941335
(example app id, don't use it)
Getting the code
You can then get facebook to generate the comment code for you
You then need to paste that code into your page, correcting the appid if its wrong ( I have multuple app id's so it chose the wrong one)
The code will look something like this :