Marcos,
The comments box that EasyBlog inserts should work ok with JFBConnect. Looking at their code, they *do* re-include the Facebook Javascript library which could a) cause a conflict on your page with the login functionality of JFBConnect and b) slow down the page load a little since there's extra to load.
However, if you test and things work for you, it should be alright. Our Google Analytics, email notifications and other features should work with their comment box.
I hope that answers your questions,
Alex