how do I run a debug session for a TPM executable?

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I have a Atmel-8528-TPM-I2C-SPI-Development Kit. I am trying to figure out how to debug the sample code that came with my development board. I already verified that I can connect my board to a JTAG emulator, and query the voltage from Atmel Studio. What I am trying to figure out is where is the console for interfacing with the executable? This program is already loaded in my board by Atmel. I imported the source into Atmel Studio, and wanted to modify it. So I want to perhaps change some of the printf() statements to validate what is running on the board is what is in my project. And the reason I asked about the console is that the program gives you a number of options, and you choose them. When I run the program normally ( as opposed to a debug session in Atmel Studio ), I connect the board to the laptop vi a USB port and use putty to communicate with the board.