You need to run bossac to upload things to your boards.
bossac -e -w -v -b image.bin
Replace image.bin with the name of the bin file you want to send. You'll need to find bossac on your system but if you have the Arduino IDE installed then you have it somewhere. On my linux machine it is in ~/.arduino15/packages/arduino/tools/bossac/1.6.1-arduino
That will upload the main binary file. Now, for the other binary for wifi it sounds like you need to run lua or something. I can't talk more specifically about a wifi module I know nothing about.