The microcontroller is to be mounted on the top side of the PCB.
Flash the microcontroller before you touch it with a soldering iron. For more information about verifying the working of your microcontroller, read How Do I Test My Microcontroller? This way you can make sure that it works, and can return it for a working one in the event that you received a broken microcontroller.
Align the microcontroller with the outlined columns of pads. Which pair of rows you need to solder the controller to will be different depending on which half you solder it to. The microcontroller always faces with its backside up: its components will face down, closest to the Kyria PCB.
Take a break! Many people run into issues at this part, so read over the instructions entirely before soldering, and make sure you place the controller on the top side of the PCB with the controller's components facing down. Of all the components in a keyboard build, the microcontroller is the most difficult to desolder if you make a mistake. Soldering it on won't be difficult if you follow the steps right, just take your time.
Insert the header pins on the top of the PCB in the areas marked with a white outline. You can hold the headers in place by placing the microcontroller over the headers, and then applying some tape across the headers onto the PCB as shown below.
After holding it down, solder the headers onto the PCB.
You'll be placing your components within the outlines on the top of the PCB. This means that when soldering, you'll be soldering the pins outside of the outlines as shown below.
When you use an Elite C, it might not sit fully flush with the headers because of the height of the USB C jack. This is normal and will not impact the functionality of your Kyria.
Then, solder the microcontroller to the headers on the top side of the PCB. After soldering the headers, you can trim off the excess header pin lengths using flush cutters.
When trimming the legs, take care to wear eye protection. I prefer to wear a protective working glove, and place my hand close above the cutting area to prevent tiny sharp bits of metal from flying around. The glove will keep my hand from being hit by the pieces. They can be quite sharp!
If you'd like to socket your microcontroller, you can check out the detailed guide at How do I socket a microcontroller?
For the Kyria, both controllers are installed on the top side of the PCB, with the components on the microcontroller facing towards the bottom.