The way its configured on the diagram the middle pot controls the tone for the neck, and the last pot controls the middle. Which one do you want to control the bridge tone?
Take the black wire, (green arrow), and move it to the terminal with the red arrow. (As shown on the right side.) That will give you the middle tone knob for the neck, and the N/M. The lower tone control will give you tone control for the bridge, and B/M. You'll have no tone control when the middle is used by itself. There's no way to get around this since one side of the 5-way is being used for auto-split. A Superswitch could do both.