Just go to the "Map Controllers" page in the game and press the "Default Map" button if you want the game to set the base defaults. You will still need to program the throttle, rudders and so on, to commands.
Or you can check in the "Map Controllers" page to see what did not transfer over and manually correct it.
In some cases there was simply no way to transfer the settings to the new format. It is explained in the README for the update.
If you are still lost, then maybe
this will help.
