How do I assign artwork pieces to acrylic layers?

Every piece defaults to the first engrave layer (the second color) — nothing is placed on the bare top surface automatically. To change a piece: select it (Ungroup a grouped SVG first so you can pick individual paths), then use the Top / Mid / Deep swatches in the selection toolbar or the Layers panel. Top returns the piece to the bare top surface (negative space, no engrave); Mid is the first engrave layer; Deep is the bottom layer (the second, deeper engrave). Your choice sticks — the automatic default will not override a piece you have assigned.