Sorry, but I had to move your post, as it didn't belong in the Schematics section.
As to your question, we're going to need more info about what guitar this is going into. How many pickups? Are the others also SD pickups? Do you intend to split the coils of the Hot Rails? What switching is there?
And, more basically, what exactly is the confusion?
As a general rule, SD pickups have the black wire to the "hot" output (i.e., generally to a selector switch or to a volume control). The green
goes to "ground". The red and white wires are generally wired together and the connection is taped off, unless the coils are wired to be split.
But, you'll notice a number of "generallys" in the above statement, to eliminate those and to focus on exactly what your guitar is supposed to do, we'll need more info, as detailed above.