You will need:
Separate the four foam pieces provided with the Pixhawk kit, and attach them to the bottom four corners of the board. Mount Pixhawk to the Pixhawk plate with the arrow facing as shown below (towards the less elongated end of the plate).
The switch (button) snaps into the round hole in the accessory plate. Disconnect the switch, thread the cable through the hole in the accessory plate from the top, and gently pull the switch into place. Reconnect the cable to the SWITCH port on Pixhawk. Using double-sided foam tape (not included), mount the buzzer to the underside of the accessory plate.
accessory plate bottom view
Place the base of the GPS mast over the four holes in the accessory plate with the shorter side facing the left side of the plate (the arrow-shaped holes in the plate face forward). Add a mounting screw to each hole, and secure with nuts.
Remove the adhesive backing from the mast and place GPS onto the mast with the connectors facing the shorter side and the arrow on the GPS pointing in the same direction as the arrow-shaped holes in the plate.
Use zip ties to secure the hanging cables to the mast.
Follow the instructions here to wire the Pixhawk autopilot system.
Add a 5 mm nylon bolt to the four holes in the accessory plate marked below, and attach a 30 mm standoff to each one below the plate. Add the Pixhawk plate to the ends of the standoffs and secure with metal nuts.
Place the assembled plates over the exposed bolts in the top plate, with the arrows facing towards the blue arms, and secure with metal nuts.
Select a location on the copter to mount the I2C splitter, telemetry radio, and RC receiver. Use dual lock or double-sided foam tape to mount the components. Check that all components are connected securely to Pixhawk. Where you place the components on the copter is ultimately limited by the length of the cables between modules. Experiment with the different length cables provided with your kit, and find the best place for each module on your copter.
(mast not pictured)