When It cames to connecting the controller ports up, I didnt use the cable which was supplied with the RetroPie GPIO adapter. I used female dupont GPIO cable so I could easily remove the controller ports if needed and it made everything look a lot neater.
I soldered the end of the cables to the correct pins and I missed out the resisters. I traced the pins from the image of the layout below and soldered the end of the cable to each one which is needed only 5 out 7 pins are needed.
After you have soldered the cables to each pin I used both images below to know which pin connects to which pin on the RetroPie GPIO adapter.