Understanding software handling

Hi all,

I am really very impressed how many information about software and hardware configuration for my Arducopter I can find in the manual on the site diydrones.com. It is really a great job, thanks for all the people involved!

But as a beginner in electronics I am a little bit confused when I try to change some basic things in the configuration. 

Could you please explane to me, how it works in general?

1. My copter is already configured with MissionPlaner. And when I want to change something in the Arducopter files (e.g. config.h) where can I find the files on my hard drive? Are they exaclty the same as they uploaded in the copter?

2. How should I upload the changed file? Is it possible to do it with the Arduino software? Is it possible to upload only one file or should I upload the the whole set of files (*.pde *.h)?

3. When I upload the whole set of files, what will happen with the settings which are already done in the files which were previously in the APM? Will they be lost and replaced with the new configuration (all new settings made on files *.pde *.h?

4. When I change something in the MissionPlaner (e.g. PIDs, TX settings and so on), how should I upload the changes? Will the files *.pde *.h placed on my hardware be changed to?

I would be very grateful for getting answers for my questons.

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