I don't know exactly what you want.
facebook comment and wp comment are definetly different comment system database.
if you use this plugin, it will save (not duplicate as you said above) the comment made by facebook to wp comment database. Because everyone know that fb comment use iframe (iframe are not crawable by search engine). That's the default setting created by this plugin ( you cant change it).
you only have two option.
1. You can set the comment to auto or manually saved to your wp comment default.
2. You able to choose whether to show or not the default wp comment side. If you set to not show, then only fb comment will appears to visitor. The wp comment default will be hidden but still crawable by search engine (good for seo).