You can stop/launch the DSC Engine from a remote application using the VI Server.
A remote VI can launch the engine using the Launch Engine.VI or stop it using the Engine Shutdown.VI.
They are located at
C:\Program Files\National Instruments\LabVIEW 6.1\vi.lib\lvdsc\_engine\User\
If you are going to use VI Server, just make sure that you enable the VI Server on the Computer that has the Engine.
There is also an executable that launches the engine called DSCEngine.exe located at
C:\Program Files\National Instruments\LabVIEW 6.1\
that you could access remotely if you share the LabVIEW 6.1 directory. This executable can be used to launch the engine also.
I would recommend using the VI Server, since sharing the LabVIEW directory might not be a good idea.
