Hi Nick,
Great question and this reminds me that I need to add more detail on this topic to the site. For your version of the DAQ PCB, SMA 3 can take an input trigger to start and stop Miniscope recording. First you need to check the 'Trigger Ext' box in the DAQ Software which will disable manual triggering and enable external triggering. The system will now start recording on the raising edge of the input signal running to SMA 3. This signal can be TTL, LVTTL, or CMOS (basically digital signal who's high voltage is over ~3V). The recording is stopped on the falling edge of the signal. In order words, when the external trigger is high the system will record, when it is low it will stop.
Hope this helps.