Thanks to the replies below my workflow has been simplified to:
Plug phone in via USB
Build and Run
When done plug into GearVR
If I only want to test it using my Android controller without gearVR on the note the Unity Remote app works well.
To fix the issue with the upside down camera, I needed to check Flip Y on the OVRCameraController.
The issue with the Unity editor crashing upon pressing stop has to do with the OnDestroy method in the OVRDevice script if you have the DK2 config installed (see other thread for more details).
I am having a couple of issues with my installation of Unity + Mobile SDK Prefabs and Blocksplosion example.
After pressing Play in Unity to start game testing my copy of Unity crashes, I can typically play test but if I try to Stop debugging or click in the inspector Unity crashes.
This seems to only happen if I have included the mobile OVRCamerController or OVRCharacterController prefab in my scene. My other DK2 projects work fine with no crash.
This has caused me to reload my project over and over again or after every-time I want to debug.
I am using Unity Pro 4.6.3p1
Another issue I am having is the Camera seems to be upside down when viewing output with the DK2 or on my Note 4 (using the Unity Remote 4 app).
If anyone has a link to a good workflow for debugging Gear VR apps using Unity I would love to see it.