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Setting - I am not a programmer, and haven't retained one yet to ask this kind or questions.

I downloaded the system and have a site up and functioning (www.QuiltingExpertiseCo-op.org). We are making a list of things we may want to upgrade on the system (several of which are unlikely to ever be added to the system for others).  We are also extremely interested in adding features that may be added to the system in the future - e.g., badges.  

However, if we make changes in the system ourselves, do we preclude being able to later download an upgraded version. Alternatively, do we just keep a good record of them, and then re-make them again if we download an upgraded version.

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The solution to the problem is to write as many of your changes as possible as plugins, rather than changing the core Q2A code. Of course, this won't be possible for everything, but Q2A 1.4 is introducing several new ways in which it can be extended via plugins. As time goes on, I imagine more ways will be added. For things that can't be done via plugins, yes, you should keep good notes of changes you make to the core, and reapply them to future versions.
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