Rewiring Garage, building grounds
The sub panel will need the ground to be separated from the neutral. The only place they are joined is inside the main breaker panel. This prevents open neutrals between the main and sub panel from sending current over the ground, and possibly electrocuting someone if a better path to ground can be found.

For the 3 way switch, I'm guessing you need to trace more wires, or you have a smart switch of some kind. You'll need to check the switches first, and then start tracing the cables on each end to see where they go. I'm guessing a second line is running just for the 3 way switch that you haven't found.