Thank you for contacting us on our forum.
As off today there is not possible to automatic sort your configurations. I can understand that this would have been helpful in your situation. I will register a work order on this and we might be able to do something about it in a future release.
At the moment, the easiest way to sort your configurations is in the config file. You can copy paste the lines there in your desired order. Take a backup of the config file before you start.
The config file can default be found here C:\Program Files\Techsoft\PixEdit Server\InputConnector and is named "InputConfigurations.config".
Hope this helps for the time being.