i used 3/4" plywood but you can use whatever material you like.
the cut files are 1 the layers to be stacked and 2 the top/bottom.
all tool paths are meant to go entirely through.
i picked up dowels at the hardware store and i liked using these mainly to keep it aligned while assembling.
i would suggest using a silicone based glue toward the inside of the box and a construction adhesive toward the outer edge.
solid slabs of wood are a much better option if you have them available both for avoiding plywood voids and appearance if you intend to use this design as a bookshelf speaker.