Katy, The washers do not deflect, they are too stiff. They act like a suspension system and rock to accommodate slightly different thicknesses of the flanges. The concave side should be against the manifolds.
What ever torque you decide to use, tighten the nuts a little at a time so that the manifolds stay flat. And check the torque after an initial heat and after 100 miles or less. You will be surprised by how much the gaskets compress. Don't use the paper gaskets, use only the composite gaskets made up of a copper sandwich. Make re torquing part of your maintenance procedure.