If you need to send out digital triggers with 1ms accuracy I would recommend doing hardware timed digital output assuming you have a DAQ card that supports it. Most M-Series cards do. With this type of output task you can provide a digital waveform that is output timed to an external clock. You can use one of the DAQ cards on-board counters to generate this clock. It sounds like 1kHz would work for you Then a sample in the digital waveform would output each ms. An example of how to setup the digital task can be found in the LabVIEW Example Finder. Go to Help >> Find Examples… >> Hardware Input and Output >> DAQmx >> Digital Generation >> Write Dig Chan-Ext Clk.vi. An example of using a counter to generate a clock is under Hardware Input and Output >> DAQmx >> Generating Digital Pulses >> Gen Dig Pulse Train-Continuous.vi.
Since you said you were new to LabVIEW and DAQmx the Developer Zone article, Learn 10 Functions in NI-DAQmx and Handle 80 Percent of Your Data Acquisition Applications, is a great resource for getting started with DAQmx.
Please let me know if you have any questions and take care.