No, you should make the single configuration.
Once you started your configuration, you can continue it in any moment uploading your created file to the configurator.
Why it is "much easier to program and debug each section separately." ?
It's simple configuration that no need any "debug". Once you assign any input it will work as needed.
And you don't need to open the data.cfg file and change anything in it. This is a simple list of assigned parameters, all work is done in the plugin, which interprets each parameter depending on its function and type of device or plane.