Hi tst-
Absolutely! The settings in MAX are only for testing purposes and do not persist when you close MAX. For examples of how to read and write to the digital lines in LabVIEW, check out the examples (Help>>Find Examples) called "Write Dig Chan.vi" (Hardware Input and Output>>DAQmx>>Digital Generation) and "Read Dig Chan.vi" (Hardware Input and Output>>DAQmx>>Digital Measurements).
You can configure individual lines for input or output by entering "Dev1/port0/line0, Dev1/port0/line3" and so on for a non-contiguous list of lines or "Dev1/port0/line0:3" for a contiguous list from 0 to 3.
Hopefully this helps-
Tom W
National Instruments