1) Yes, this is completely separate from JomSocial's integration, which should be disabled if you enable JFBConnect. There are a lot of differences in how we operate, mainly by allowing more control of how integration occurs, but nonetheless, separate.
2) There's 2 answers to this. The first, and the bad news, is that we currently don't import existing connections into JFBConnect from JomSocial. Our next update (version 3.1) should automatically import those connections, which is due shortly. The 2nd, and good news, is that we have an option to automatically connect Facebook users to a Joomla account on your site if their Facebook and Joomla email addresses are identical. This may not work for all your users if they've changed the default email.. but even if they have, we have a Login or Register page that can be used after they connect with Facebook to specify the Joomla account already existing on your site.
3) We require the API, Secret key, and Application ID for JFBConnect to function. If you use the same keys as you had in JomSocial, then any user who previously approved your application won't need to do so again.
Hope that helps, and if you have any more questions, just let us know!
integrating into existing site with JomSocial Connect
