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: it will be different depending on which half you solder it to. The microcontroller always faces with its backside up: the USB port will face down, closest to the Kyria PCB.
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.
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 USB jack facing towards the bottom.