Unfortunately you will have to flash them all one by one. I mean, I'm not saying that it is impossible to flash more than one board at the time but all the flashing methods available were designed to flash one board at the time.
You also would like to add some packages after flashing the board. You could avoid that step by creating your own image by following the steps in the BSP. That way you can flash the image with the latest MRAA, UPM, etc. already installed.