1. Including a JTAG header is advisable
2. No you not need the FTDI chip...even on the CRB you have the option to bypass the the FDTI using a debugger - Olimex and Flyswatter2 configuration files are provided.
3. To debug you will need either the Olimex or Flyswatter2 debugger and related cables.
Alternatively it is possible to use the D2000 CRB to Flash/Debug :
This is the procedure that needs to be followed ...
a.Remove all sleeves from jumpers J9,J10,J11,J15. J17 on the D2000 CRB
b.Power on your board
c.Make a 1:1 connection from pins on the D2000 (Pin's 2,2,2,1,1 on J9,J10,J11,J15. J17) to your board.
b.Connect the CRB as normal and flash using ISSM (Choose USB-Onboard as the connection Type)
In addition to the JTAG flashing you also have the option of using DFU over UART on the D2000 - see this doc of details - http://www.intel.com/content/dam/www/public/us/en/documents/guides/software-interface-bootloader-user-guide.pdf
Details on how to use this utility in the latest version of ISSM are available here (the DFU utilities for UART are included in the installation so no further download is required) - Intel® QMSI Firmware Manager | Intel® Software
Note that this option is available for the Firmware Application only -- not the Bootloader(ROM).