The white wires (commons) will go into to common wire ports, which are marked by "C", on your Rachio controller. Make sure to put them into different ports and not two into the same port!
The black wire (P/MV) will go into your master valve port, which is marked with a "M". Make sure to enable your master valve in the app while getting set up!
The rest will just go into your zone ports no problem. Attached is a diagram of the wiring ports to help you out, let me know if I can answer any other questions!