Transitions have edit handlers which can be manipulated. The beginning and ending stations can be dynamically moved or values can be keyed into the edit fields. Keep in mind if you move a transition (which is adjacent to a template drop), they need to be moved individually. For example, if the transitions ends and a template drop starts at 14+00, and you need the station changed to 13+50, you need to move the transition and the template drop individually.
To manipulate the transition, right-click on the transition and select Edit Transition from the context sensitive menu.