Wire up the components according to the schematic. For the design to work you'll need to place the buttons, neopixels and encoder as I did on a perf board 15 x 26 (holes I'm counting here).  The buttons can be placed right at either edge and 1 hole up and the middle one in the middle at the bottom.  As for the encoder I have in the 12th from the bottom and placed in the middle with the Xiao at the very top so the USB-C port lines up.  Neopixels arent as fussy but somewhere in line with the encoder and at the edges of the perf board.  I've also drilled some 3.5mm holes in the board for the screws to pass through.  Just make sure your jumper wires dont pass over those points. 

Print the components.  I used transparent for the buttons and the knob for the neopixels to shine through and black for the case.  It worked well as the black doesnt allow the light to pass through.  

Assemble the 3d printed pieces of the case.  The buttons should go on first, top down.  They should fit but depending on your printer might require a little filing or deburring around the holes.  Then the board in next and the bottom and then screwed in flush with countersunk 20mm M3 bolts.  Then the encoder knob should fit snugly onto the encoder.  

Download the Arduino sketch and Companion App from the github page.  You may need to add the Seeeduino board libraries to arduino and follow their instructions on setting it up (by the way it also works with the Adafruit QT Py).  Upload the sketch.  Once its uploaded, run the Companion App.  You may need to click on the icon in the notification toolbar to set the port. The app records the VID and PID of the device so it should know to connect to it regardless of port afterwards (in case you use a hub).  There is an ini file with the compiled exe that sets some default settings.  I planned on putting in more colours and config keys in here, but I didnt see the point as it was only really compiled for me and I can make changes just as quick in Visual Studio.