Hi Jason,
If you are just targetted to the device and running the VI directly from the LabVIEW development enviroment then you need to make sure that when you close LabVIEW you choose "Exit without closing RT Engine VIs" form the File drop-down menu. If you are creating an application and embedding it onto the target then the tutorials I referenced you to talk about how to have it auto run upon boot up (typically the default).
Regards,
Bryan Snarr
Field Engineer
Northern California
National Instruments