Which Arduino IDE were you using? I just tested the Arduino IDE 1.6.5 with the x86 boards installed from the board manager on OS X 10.11.2 El Capitan and I was able to successfully upload the blink sketch to my board. I'm currently using the latest image found in Intel® Edison Downloads.
Have you tried with Arduino IDE 1.6.5?
Were you able to flash your board with yocto 2.1 on your mac
Were you able to flash your edison board with yocto 2.1 on your mac? and were you able to see your board in the flash tool window?
I am attaching a screenshot of whats happening to my flash tool as well, I was able to flash it using terminal but not with the flash tool.
I also use Arduino on Mac OS X El Capitan.
Which PORT do you use ?
I set PORT to cu.usbmodem.xxxxxx
You can see from the image /dev/cu.usbserial.xxxxxxx
So, you are saying that i should change the port cu.usbmodem.xxxxxxxx