If I were to follow the following tutorial, would I solder the wires to the top two terminal points so that the neck on mod would only work when the push push is pushed up?: 
In the following tutorial, why is one wire directly from the pickup and the other wire from the output?

To fulfill your request for modding your Yamaha Pacifica 112J so that the neck pickup works normally when the push-push pot is in its default position, and can be added to any pickup selection when the pot is pushed, follow this guide. Yes, this wiring mod will work and allow you this flexibility, giving you the ability to "override" the pickup selector switch to include the neck pickup with any other pickup(s).
Materials Needed:

    Push-push pot: Ensure the pot is suitable for replacing one of the controls, typically the volume pot, and is the correct value (usually 500k).
    Soldering iron and solder
    Wire stripper and cutter
    Screwdriver
    Additional wire: At least a foot of insulated wire, likely 22-gauge.
    Heat shrink tubing or electrical tape: For insulating the connections.

Steps:

    Prepare Your Workspace:
        Ensure your guitar is secure on a stable surface and your tools are organized and within reach.

    Replace the Volume Pot with a Push-Push Pot:
        Carefully remove the knob and unscrew the existing volume pot.
        Disconnect the wires from the old pot, taking note of the wiring (consider taking a picture for accuracy).
        Install the push-push pot in place of the original volume pot.

    Wiring the Push-Push Pot:
        Normal Operation (Pot Not Pushed):
            Connect the neck pickup’s hot wire as it was originally, allowing normal operation via the pickup selector.
        Override Function (Pot Pushed):
            Connect a wire from the neck pickup's hot wire (where it leads to the selector switch) to one of the switch terminals on the push-push pot.
            Solder another wire from a different terminal on the switch section of the push-push pot directly to the output path (before it splits to tone and volume controls, or directly to the jack, depending on your preference).

    Grounding:
        Make sure the body of the push-push pot is grounded. You can do this by soldering a wire from the pot casing to a grounding point in the cavity.

    Testing:
        Plug the guitar into an amplifier.
        Test the neck pickup in its normal position using the pickup selector.
        With the pot pushed, check that the neck pickup can be added to any combination of other pickups using the selector.

    Reassembly:
        If the mod is functioning correctly, insulate any exposed soldered joints with heat shrink tubing or electrical tape.
        Reinstall the control plate securely, making sure all components and wires are correctly tucked in.

Final Notes:

    Safety Practices: Handle the soldering iron with care, and work in a well-ventilated area.
    Use of Diagrams: Refer to wiring diagrams for your specific guitar model if necessary.
    Professional Consultation: If uncertain about electronics work, a professional guitar technician can ensure the modification is completed correctly and safely.

By following this guide, you will enable your neck pickup both in isolation (using the selector switch) and in combination with other pickups (by engaging the push-push pot), providing you a versatile sound palette.