>Should I... Place one hive brood box directly on top of the other
>after the bees have clustered.

That is what I do.  Place the heavier one on top and rotate the 
boxes so the clusters are lined up above and  below one another.

If the bees are torpid when combined and no great disturbance is 
made, there should be no fighting, and the two clusters should 
unite over time when it warms up.

You should be able to do this even in cold weather as long as you 
are deft, don't blunder around or drop boxes and bees.

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