Install the latest beta (as of this writing 1.3.0+beta2) of our software (see beta post for instructions) and download the Release Candidate 4 (RC4) or later of the Arduino 2.0 IDE.
With RC4, the Arduino IDE has a patch we wrote to fix a bug in the pluggable discovery feature of the IDE. With this fixed, we enabled that functionality in our 1.3 software version. So now, when you list the ports available, there is a special 'qNimble ports' section that will only list the main Quarto port.
In addition to it being easier to select the right port to communicate with the Quarto, now the Arduino IDE should much more reliably stay connected to the right port when flash new code.
If you have any issues, please post here.