The PCB comes pre-programmed with the standard layout that can be seen here. To make sure the PCB is (still) functional, plugging it into a computer should result in the green LED being lit-up. If it doesn't, you may need to make sure your computer is treating it as an actual keyboard (let it install drivers/click confirmation boxes) and giving it power. This shouldn't be a problem for most machines.
OPTIONAL SIP INSTALLATION
If you've opted to place SIPs in your keyswitches, and you're using a closed plate (non-universal, like the MIT plate), now is the time to do so! If you're using an open plate (universal) or none at all, these can be installed anytime afterwards.
Remove the top of each keyswitch by allowing the 4 "claws" to pass over the bottom half's lips. It's much easier to place the SIP while holding the switch top slightly above the bottom, keeping the spring and internal mechanism aligned with each other. Once the SIP is in place, you can carefully place the top back on.
Once you've ensured that the glowy bits are glowing correctly, you can get started on assembly! Placing a few keyswitches into the plate (if you're using one) and then pushing the PCB (the nearly blank side) onto those few is the preferred method to seat the PCB against the keyswitches correctly. Putting all of the switches in the plate, then pushing the PCB onto all of them is very difficult, and can lead to errors with the pins.
Once you have a few switches in (start with the corners) and the PCB attached, you can carefully place the half-assembled unit into your case (if you have one) to finish placing the switches. Inspect each switch with a quick clicky-clicky and make sure the pins are sticking out straight - it's semi-difficult to remove the switches after placing them.
When done placing the switches, remove the keyboard from the case and inspect the pins sticking out from the board - you should be able to feel/see all of them sticking out the same distance. If the distance varies at all, it may be an indication that the PCB isn't seated correctly. Pressing carefully but firmly on the PCB/switch (watch out for components) should help it to travel as far as it can - you may hear a satisfying click once it's in place.
If you plan to install 3mm LEDs (without SIPs), now is the time to do so! Looking at the bottom of the PCB (the labelled side), you should be able to see a + or - by every LED pad. As a reminder, the longer end of the LED needs to be aligned to the + side. Pay attention as the orientation varies a lot on the bottom row.
If you're using SIPs, you won't need to place the LEDs now - that can be done once the board is complete. Be sure to be mindful of their orientation when installing them, though.
You'll always be able to install LEDs later on - there's nothing preventing you from doing that in the future.
If all of the pins are sticking through the board, you're ready to start soldering! Make sure your soldering iron is hot and you have some good ventilation. Turning on an adjacent fan is recommended so you're not inhaling/exposing yourself to the solder fumes.
When soldering each pin, it's best to place the tip of the iron on the pin/pad and push the solder into the intersection of the two. Getting them hot helps the solder to form a good connection. Try not to get solder anywhere but on the gold pad, and be sure not to form any bridges with nearby components. Doing so may cause random key presses or break things (temporarily, likely).
The size of the solder you're using is mostly unimportant, but it's recommended that you use a smaller gauge (smaller in diameter), as it will be easier to control the flow. It is recommended that the solder be rosin/flux cored to help it flow onto the pads. Additional flux may be used, but shouldn't be needed.
You'll be soldering 2 pins for each keyswitch, and 2 pins on the LEDs/SIPs, if you're installing those.
Once you have all of the pins soldered, you'll want to inspect each of them to make sure the solder has correctly tented over the pad. The PCB is not prone to many errors (unlike hand-wired builds), but they can happen.
If you're sure everything looks good, place the keyboard into its case, and plug it in. Pressing on a keyswitch should result in some action, so open up a text editor to type into. Pick a switch in the middle of the keyboard to make sure it'll be a letter, and not something unexpected. If it looks like you're getting something, go ahead and test every switch to make sure each has a good connection. Some switches may be modifiers or the LED control.
To test the LEDs, press the key in the lower left-hand corner until the LEDs light up. Pressing the button cycles through the various levels in the firmware (0-4) - it may take a couple of presses to be able to see the light.
If all is working, screw in the screws to your case, and close it up! If you're using the milled bottom, you'll be able to reset the board for flashing with a paperclip after everything is sealed up. If you're not, you may want to hold-off on closing things up until you've successfully programmed it.
Once screwed into place, stick some keycaps on that thing, and call it done! The screws can be difficult to place once the keycaps are on.