I just did this a couple of months ago. Next time we'll try to document it better.
You need a system running Ubuntu 14.04 to install the Jetpack on. A vm might work but I haven't tried it. I did manage to get it work from 16.04, but I would stick to 14.04 if you can.
The current Jetpack documentation is here:
http://docs.nvidia.com/jetpack-l4t/i...4t_install.htm
Make sure you install OpenCV for Tegra and CUDA toolkit. You might not want to install some of the samples or machine learning packages.
The install will walk you through putting the board in recovery mode.
Last year we used two builds of our code. One with a GUI to view the processing for calibration and one without the GUI. We would ssh with X forwarding into the TK1 to use the GUI version.
Our code with here:
https://github.com/FRC-Team-4143/vision-stronghold
It documents most of the tweaks to the standard configuration we used. I need to clean up a couple of symbolic links in /etc that git didn't follow.