At the moment, the only way I know to do this is:

var subGeometry:SubGeometry = new SubGeometry();
mesh.geometry.addSubGeometry(subGeometry);

// find which SubMesh has this SubGeometry
var subMesh:SubMesh;
for each (subMesh in mesh.subMeshes)
{
if (subMesh.subGeometry == subGeometry)
{
break;
}
}
// assign proper material to this subMesh
subMesh.material = your_material;

There should be a slightly better interface coming to achieve this at some 
point. This isn't ideal, I know.

-Dave

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