Here are some basic directions for getting your laptop connected to your JB4, updating the firmware, and doing a datalog. The JB4 software only runs on Windows so if you have a Mac you will need to use boot-camp or parallels.
To connect to the JB4 you'll need a BMS USB cable available here: http://www.burgertuning.com/JB3_upgrades.html
For the USB cable routing/install you have two options. Option 1 is to route it over the rubber grommet under the DME cover and leave it there for quick access.You'll just have to lift up the one snap on black panel and can then route it in the window or door jamb on an as needed basis. Option 2 is to route it in to the glove box which takes 15-20 min or so and requires DME removal. There is a DIY here: http://www.n54tech.com/forums/showthread.php?t=6557
To update your firmware download the HEX file from the bottom of the JB4 post and save it to your laptop desktop or a thumb drive. Then once connected press upload firmware in the interface and select the HEX file to upload it. If updating from older firmware also press the "restore defaults" option in the interface while connected to update your settings to the current default settings.
For datalogging you'll connect and start logging. Then do some wide open throttle runs, like 40-100mph on a safe private road, and 2000-7000rpm in 3rd gear, and finally export to CSV. Email that CSV file in to BMS if you need technical assistance. The logging will run for up to 8 minutes per log so keep that in mind when starting a log.