Yes, the wires from the NMRA plug go to the decoder's 8 available connections (but you will only use 4 of the connections, since you only call out 4 wires available). The blue wire can go to either of the common connections (+12 V) and the white, yellow, and green wires go to the function terminals marked 1, 2 and 3, respectively. These 4 wires carry the common (blue) used for function power and function control (white, yellow, green) from the decoder to the Atlas motherboard.
Scott