Can you save layers only?

Lets say that I want to make a 3 layer design. One layer for the back, one cutout for the middle and then another layer for the upper piece. Is there a way to save each layer separately or do I have to save them all as a single project and then turn off each layer when I go to cut them out?

You don’t “have” to save all three layers as a single project. If you want to have each layer as a single file, there is no reason you can’t do that. For my money, a single click to output or not is more efficient requiring less clicks to complete a job and all objects for said job are then stored in a single file/location.