1. Drill large holes in all the same size pieces but one, and put that on top. Probably needs to be fairly large holes, and plenty of them.
2. Or stack glued up pieces in twos, threes and fours--or however many you typically stack.
3. Or stack them and drill 3/8ths holes in all 4 corners, then cut 3/8ths dowels to lengths just shy of the heights that will fit and be just slightly below the top layer's surface. You'll have a lot of dowels, but dowels are cheap. Slight sanding may be needed to have them fit. Clamp BEFORE you drill the holes.
I am assuming you want the top layer to be smooth and flat for free movement of the router. Suction will hold the stack in place, but you could drill positioning holes through the bottom layer and the top of the sanding box, put a positioning pin in the bottom layer, and the whole thing will be in register.