The instructions for assembling the Pi v3 and the previous acrylic Pi SAFE are quite similar. Only difference between the models is the location of the LED light pipes, so these Pi3 instructions apply generally to all Pi SAFE versions.
Find 4 of the 4-40 x 3/8" bolts, and put them through the baseplate, and press the spacers on from the other side. Thee bolts will sort of stay put until you can get the Raspberry Pi on the baseplate. (If adding to a VESA mount, do only 2 diagonal screws)
Slide the Raspberry Pi onto the bolts. The Pi is designed for metric M3 hardware, but we're still using imperial #4 hardware, which is a smidge bigger. The bolts may need to be screwed through the holes in the Pi.
Add the #4 nuts, and tighten them down.
Arrange the sides as shows. The sideplate on the top in this image has the long cutout to accommodate a ribbon cable from the 40-pin expansion port. The front faceplate on the right (with the lable engravings face-down) is for the communications side. The sideplate on the bottom has the ports for the power, video and audio I/O.
Align them all up on the baseplate, and use a pair of 4-40 nuts and bolts to lock them in place.
Lay the final side faceplate face-down beside the assembly, and pop the clear lightpipe parts out of their holder. It is not necessary to strip the paper off this part.
Sandwich the two lightpipes together, and push them into the lightpipe indicator hole. They will sit a bit loose until the faceplate is attached to the baseplate.
Carefully assemble this assembly to the baseplate, and finish attaching it with the remaining 4-40 nuts and bolts.
Notch the top plate into the slots in the rear faceplate, and gently flex the frontplate out to let the tab snap into place. You're ready to power up, with full access to the indication LEDs on the Pi mainboard via the lightpipes!