Installing Gutter Leaf Guard Under Shingle
I am assuming that you are installing a surface tension type of system.  Ideally the metal sheet should go under both layers of roof.  It is hard to tell from the photo but it appears that the gutter may be high relative to the first roof.  If this is the case it will still work if it goes under the top layer only.  If the gutter is too high, preventing the gutter guard from laying at the same slope as the roof, you will need to relocate the gutter at a slightly lower position.  If the guard does not have enough slope the leaves will get hung up rather than being washed off the roof.