Normally, Autotune can set the Migrations automatically for you. Facebook recently changed the behavior of their API slightly which broke that ability for some users. If you simply hit "Save Custom Settings" at the bottom, JFBConnect will try to set the migrations to the recommended values. If you get a red error box saying "An unknown error occurred", that means the migrations couldn't be set.
From there, you can either wait until JFBConnect v5.1 is released next week and use Autotune then, or you can set it in your Application manually. The October changes are a ways off, so it's not critical that that value is set correctly right now.
I hope that explains, but if you have any other questions, just let us know.
Thanks,
Alex