By default, the turtlebot software is currently configured to work with Kobuki. For the most part, the kobuki will work out of the box. If you're doing a manual deb or source install though, there is one last step remaining.
Kobuki needs to transfer a udev rule so that it can reliable detect the factory flashed ftdi usb chip. This enables it to be read from /dev/kobuki instead of the unreliable /dev/ttyUSBx devices.
If you have a notebook purchased from a distributor, they may have already applied the udev rule, otherwise:
> . /opt/ros/indigo/setup.bash > rosrun kobuki_ftdi create_udev_rules
# From the devel space > . ~/turtlebot/devel/setup.bash > rosrun kobuki_ftdi create_udev_rules
You can see exactly how this is working in kobuki_ftdi.