Connect the audio connection cable from the output port on the Motu to the corresponding input on the computer that has Pro Tools installed on it. As noted, Pro Tools 9 is the only version that supports non-Avid/Digidesign hardware, so if you use an older version, you will need to first upgrade to version 9.
Download and install drivers from Motu's online download center. (See Resources.) The choice of which drivers to download depends only on the type and version of operating system you use. In other words, if you run Windows 7 on your computer that runs Pro Tools, you would download the Windows 7 drivers from Motu's site. Once the drivers are installed on your computer, you are ready to proceed.
Test the connection by recording audio using the Motu interface. Make sure the Motu is powered on and that you have an input device like a microphone connected to one of the Motu's audio inputs. If the Motu picks up a signal and the audio records, you can continue to use the Motu Ultralite MK-3 to record audio on Pro Tools.