If what you want to do is to program the board, then you just need to connect the USB cable to the micro USB port. Internally, the micro USB port is connected to the FTDI chip. This is used as the onboard debugger.
If what you want to do instead is to access the console, then you have to connect a FTDI cable on pins IO0 (Rx) and IO1 (Tx). I recommend you to check one of the following videos for additional details on how to connect the FTDI cable and get access to the console:
- http://www.intel.com/content/www/us/en/embedded/products/quark/mcu/issm-getting-started-windows-vide... Intel® Quark™ Microcontroller Getting Started on Windows*: Video
- http://www.intel.com/content/www/us/en/embedded/products/quark/mcu/issm-getting-started-linux-video.... Intel® Quark™ Microcontroller Getting Started on Linux*: Video
I'm not sure if that's what you are asking for, but if not, then just let us know what you would like to do exactly.
The recommended method is through FTDI. In fact, this is the method that is usually used to upload the code into the D2000 board. You could used the JTAG of course, with the Olimax or the Flyswatter 2, but the method recommended is through the USB port (FTDI).