Check the "Complete stop" box in the brake segment panel, and sleect the number of seconds for the train to stop for. To make it launch, check the "Launch" box and select the number of G's to accelerate with in the "Acceleration" box.
Yea if you provide more information about what your trying to do, that would help. I could take a screenshot of the "brake" and "transport" (launch) sections and explain what everything does if that would help.