Sorry just saw this now. No you don't take it all the way off. Just set it. Lossen all bolts and torque down.

Hey JPack I have been trying to find a way to keep the torque arm from thudding and being too noisy and I was searching google and came across a post you made early this month and was trying to make sure this is what you do to help reduce the problem:
Install Torque arm
Set Pinion angle
Take Torque arm completely off
Put the Torque Arm back On and tighten as much as possible