Program the atom module with Starter Kit with USB


I Bought the Starter Kit with USB and I would like to know how to program the Atom module.

I need a custom application in the atom module, and from what I could get at the docs, I can either program it with one Mbed device and a arduino adapter OR I just use the Atom module as it is as a host for any other microcontroller.

How do I program the atom module per se? by using the usb adaptor, or any eventual swd/jtag pins it has?