In my opinion, you should secure the bolts in the neutral position simulating when the car is at rest on level ground. That way, there is equal stress on the rubber bushing as the axle travels up or down from this neutral position. If you torque the bolts with the axle hanging down, it could over stress the bushings when the axle travels up from the neutral position. I am not sure how critical this is, it just makes sense because the rubber bushing is flexing internally. If it were a pivoting type joint, it would not matter.
As far as the bushing position, the way you have it in the picture is the way it goes up into the arm. EPC has a good picture of that in the rear axle section. The Niemoeller site should also have a good one as well.