Best practices for forking a stable build?

Hello everyone,

I am trying to get started modifying the Ardupilot code and am having some trouble obtaining a stable build. 

I can successfully build the code using these instructions found at http://dev.ardupilot.com/wiki/where-to-get-the-code/ as well as at http://dev.ardupilot.com/wiki/building-the-code/building-px4-with-make/ .  However, when I upload the firmware to the Pixhawk, the system does not operate correctly (the buzzer constants sounds and it cannot connect to Mission Planner).

I think the problem stems from the fact that the tutorials instruct you to fork the latest version of the master branch and this build is not stable. 

When I directly download a zip of a release version of the ardupilot, P4XNuttX, and P4XFirmware source code, build, and upload, I get reasonable behavior as expected. Of course, this is not directly version controlled and "off the main branch" so I think am unable to obtain new changes from the community by merging with the upstream master (please correct me if this is not true).

Are there best/recommended practices on how to fork a stable build that can "keep in stride" with the Ardupilot, PX4NuttX, and PX4Firmware projects?  It seems like the work around is to modify a release version and then integrate my custom changes each time a new release drops but this sounds less than ideal.  I'm also fairly new to Github so any pointers would be appreciated, thanks in advance!

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