Emily,
SEAWAT couples MODFLOW-2000 and MT3DMS into a single engine to solve variable density problems. Therefore, you have two options to run and calibrae your model. You either run MODFLOW and MT3DMS separately (decoupled) provided that density effects do not affect your flows, or you only use SEAWAT to solve the coupled flow and transport simulation. Of course, you may do both options either as an exercise or to make sure your flow and transport models are consistent with your conceptual model prior to transition to SEAWAT. Remember, SEAWAT does not require prior MODFLOW and MT3DMS runs, but because the decoupled runs are generally faster it is a good idea sometime to nevertheless do that.
Either way, in order to run a transient simulation in Visual MODFLOW Classic, you first have to set the Run Type to Transient Flow in the Main menu / Setup. However, if your engine is SEAWAT, transient flow is selected by default and you cannot change it as this is the onéy option. The Setup menu item under the Main menu also allows you to change your flow engine from MODFLOW-2000/2005/NWT to SEAWAT.
András