Hey @dsrc12! Now I've found some time to give you an adequate response.
First of all, awesome! It seems you are experimenting with a lot of different things, and feels great to have such an engaged user as part of our community!
It's great that you explained that your issue is when you are uploading with the Arduino IDE. As our focus is the web interface, it could have been that have been some problems with the IDE that felt between the cracks. So I've now have reviewed all the workflow on the Arduino IDE to make sure everything is working.
First of all, make sure to use the latest version of Arduino - we will not support old releases. (At the time of this writing 1.8.5)
If you are not using Windows 10, make sure to install the Windows drivers.
Then install the Quirkbot Arduino Hardware (at the time of this writting, verions 0.4.9).
Then install the Quirkbot Arduino Library (at the time of this writting, verions 2.5.7).
You should now be able to see some examples:
We recommend using the "Empty" example as a base for your projects - as it makes sure you include "Quirkbot.h" in your sketch. It is important to include that library as it does some initialisation on the board and allow's it be programmed via https://code.quirkbot.com. If you remove "Quirkbot.h" the boards will not be programmable via the web interface anymore - if that happens just upload an empty sketch that includes the "Quirkbot.h"
In case you don't want to use the "Quirkbot.h", then use the "Without_Quirkbot_Library" example - it shows that you need to call the "watchdog reset" regularly to avoid the board going into bootloader mode. (but again, I highly recommend just including the "Quirkbot.h" so you can skip those steps.
Please make sure that while you are using the Arduino IDE you don't have any tabs open in the browser with https://code.quirkkbot.com - as it will interfere with the serial communication from Arduino.
It would be great if you could test it and let us know how it goes.
Also please disregard all the the references to Codebender and Arduino Lillypad USB, those are old references that should not be considered any longer.
Very interesting to integrate with Ableton - we have a huge interest in using the Quirkbot for making music, and have made several experiments connecting it to synths. We will soon be publishing some new features that will allow the Quirkbot send MIDI messages for even more interesting integration. Please let us know how the firmata experiment goes!