Which of these diagrams should be in the copper side of pcb?
This is a design for a two-sided board. You need to have copper on both sides of the board and etch each one according to the provided pattern to make this circuit.

Edit: FWIW, I agree with the other answers and comments saying this board as drawn is not a great candidate for toner transfer. However it should not be difficult to re-design this as a one-sided design, probably with a few jumpers. Or simply pay a few dollars and wait a couple weeks to have it built for you.