Configuration file:
In GCS, Menu at top of window, File - Export UAV settings. That will save to a file which you may upload here.
Or do I have to manually save a copy of it on the desktop between changes to my drone configuration?
Since now it's an 'all the time' thing upload what you have now.
Version of Librepilot, oh, well each time I run the wizard it updates to the latest version right?
It updates the firmware in the FC. Once that's done you don't need to keep doing it.
After multiple-multiple revisions/updates of firmware sometimes it's a good idea to save UAV, do a 'Update with Erase,' and reload firmware from saved file. I don't know if that recommendation still holds, or if it is only foe CC3D or Revo style FCs.
Between that does the GCS update it self between internet access?
No it's 15.09 now and doesn't change
The most common reason for 'can't arm no way no how' is because there's no flight mode that -isn't- GPS assisted.