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I'm designing a keyboard with the Proton-C and I'm not sure about using decoupling capacitors - how to connect them.
It has 3 GND pins, 1 VCC/3.3V pin and 1 VBUS (5V_RAW) pin (if I'm looking at it correctly.) Do I use 2 decoupling capacitors, one connecting VBUS to GND and the other VCC to GND and then if something needs to be connected to GND/VCC/VBUS I connect it through those capacitors? I'm pretty confused to be honest.
The module has its own decoupling capacitors. Unless the module datasheet suggests otherwise, any extras are for whatever you connect. You've not detailed what else is being connected.
If you use both the 5V and 3.3V, you may need two capacitors, maybe more. You've not detailed what else there is - you could have 20 WS2812 leds which should have a capacitor for each led located as close as possible to each led.
