So far I have managed to avoid using green stuff. I think I was able to get by owing to the design of Space Marine models - the armor naturally hides the arm joints under the shoulders pretty well, and I wasn't doing anything spectacular with poses. Also the quality of the metal miniatures is pretty good.
But for the Vanguard Veterans it was time to learn for a few reasons. 1) First just to learn and improve my skills. 2) Also, I wanted to magnetize the arms to allow for different weapon loadouts and 3) In order to support some arm poses the backpacks had to come out away from the body a bit to fit the shoulders.
I found working with green stuff was fine for the most part for this type of work where I am not sculpting anything in particular except flat joints. Nevertheless, I picked up a set of 5 "ColourShaper" brand size 0 Clay/Wax/polymer clay silicone tipped sculpting tools. Silicone is really important because the stuff doesn't stick to it. While mixing it with my hands I just dipped my finger tips in a bit of water to keep it from sticking - that worked ok.
The results were pretty good - it seems the magnets are in there and fit for the most part. Definitely there is room for improvement in the future as some magnets were a bit too deep (and so I should have put green stuff behind them) while others stick out a bit. I tried to pair up arms with bodies such that protruding magnets would be paired with sunken ones.