Instagram configuration section?

- I am not seeing anything on Instagram labeled configuration. Where is it?

The configuration settings for Instagram are in the JFBConnect Configuration section in the "Instagram" tab.

- Also is Facebook the only application you can download profile images and profile data from to auto create an account?

The Facebook Application is used for any of the following:
* Facebook authentication and profile import for your users
* Pushing content to your Facebook Page and or Group
* Using the Channels feature to create a "Social Stream" like you can see at the bottom of this site.
* Open Graph Actions, for letting activities that users take on your site be pushed to their Timeline
* Comment moderation - If you use the Facebook Comments module, admins of your FB Application can hide posts from users if they don't want them displayed.
There are likely other things I'm missing right now, but that's a good summary of the main reasons to have an app. If all you want is to use Like buttons or some of the other Facebook widgets, a Facebook Application is not required.

- I was using Facebook Connect and many people's profiles did not import over. If an account was already created from Facebook or from the site's log in method, would the users profile update with their users Facebook profile. If not is there a way to refresh the logins so they would?

What extension are you trying to import the user's profile into? In the JFBConnect -> Profiles area, if the "Always Import Profile" setting is "Yes", then the users profile should be imported whenever they login to your site with the social network. If that setting is "No", their profile would only be imported when they register on your site with a social network.

I hope that helps explain, but if you need anything else, just let me know.

Thanks,
Alex