There's no changes necessary in your Facebook Application settings. The only changes required are in how JFBConnect interacts and requests data from Facebook on behalf your application.
The changes also only affect 'new' apps, created on August 5th or newer. JFBConnect supports those changes for all apps created since that time, as well as apps created before that time. In 2 years from August 5th, the new changes will be mandated even on the old apps. So, by upgrading, your ensuring that your ready now for the changes, whether your app is affected yet or not.
I hope that helps and makes sense,
Alex