I can't help with the MATLAB interface, but I can help explain the events on the AUX I/O port.
If you read the specfications document for your device, located here: http://digital.ni.com/manuals.nsf/websearch/F6901F4B80F39BBD86257D5B0058AFBB
you will find the specifics of what the output can do when configured. For example, the specifications state that the Logic type is 3.3V CMOS, so at most you will be able to output a 3.3V pulse, not a 5V pulse. It also specifies which events can be routed and an output event through this connector.
For more information regarding the events that can be exported, please reference the Digitizers Acquisition Engine State Diagram. In this diagram, all the red arrows indicate events that can be exported when configured. As you can see, you will need to setup a "dummy" acuisition, and it will be able to export a pulse for whichever event you configure to export.
In LabVIEW, to export an event, you use the "niScope Export Signal.vi" to configure which signal to route to which PFI line.
Using the NI-SCOPE C API, you configure the events by using the function "niScope_ExportSignal". This is similar to the LabVIEW VI. Using C, you could also configure the events to export by setting the appropriate attribute directly. See the Synchronization Section of the Functions Reference. So, if you want to export the Start Trigger Event, you would set the "NISCOPE_ATTR_EXPORTED_START_TRIGGER_OUTPUT_TERMINAL" property to "VAL_PFI_0", for example.
I hope this helps!
-Nathan
Systems Engineer
SISU