Hi John,
Flatshot will let you let you set color and linetypes to bylayer but it will not let you set any specific layers for it. I believe it always drops the lines onto layer 0. (I don't have a complex model to try this on so I am relying on some simple 3D solids I created.)

You could set the entities to a distinct color and use Qselect to select them quickly and change them to the layer you desire.
If you want to attach a sample file I would be happy to explore some more.
Please select the Accept as Solution button if my post fully solves your issue or answers your question.
John Vellek
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