Few noob questions I couldn't find in the docs:
The Monitor One isn't normally powered off, but you can do so by enabling shipping mode which is how it's shipped from the factory. To turn it back on you need to plug into an external power source. In normal operation you'd use sleep modes instead of turning it off.
The LED colors depend on the LED configuration in the console. The colors are described in the status LED and device modes page.
There aren't 3 available ADC Inputs on the I/O card. Using the prototype card, you can use available MCU ADCs, which are 0 - 3.3V only, single-ended 12-bit. Note that there is minimal protection on the ADC pins, so you may want to add additional input protection such as rail-to-rail TVS diodes.
OK, one more dumb question. How do you get the cmd box. I was able to find documentation on the funcKey but that did not react to the command on your link.
If you go to the Particle console, select Products, then the product containing your Monitor One. Click the devices icon within your product, then open the device. There's a cmd box there.
The device needs to be online (not connecting to cellular or sleeping) in order to respond to a shipping command OTA.
Yes, it is supposed to be in the Functions box, correct?
If you've replaced the Monitor Edge firmware with your own firmware that was not based on Monitor Edge you'll lose functionality including the command box.
It's highly recommended that you start with Tracker Edge or Monitor Edge for Tracker One and Monitor One instead of starting from empty firmware as you would do with other devices.
Is there a way to flash the Monitor Edge firmware from the online compiler? The Particle Workbench is not cooperating on my Linux box.
The WebIDE cannot be used with Tracker Edge or Monitor Edge.
If the Particle CLI is working, you can use that to compile and flash firmware, either OTA or by USB serial.
If you want to use USB under Linux, you might need to install a udev rule so you can do it without being root.