A typical example that would explain how this works is a trio analysis study where you want to compare variants found in a child with those from the mother and father. For this, you would create a workflow including mapping, variant detection, variant annotation and maybe some quality control. All three samples would be processed through this workflow in batch mode (see Executing a workflow). At the end, you can manually create a track list with all the relevant tracks (reads and variants) and run the trio analysis tool manually.
Since all the comparative tools are relatively quick, the bulk of the computation work can usually be incorporated into the workflow which can take care of the more tedious parts of the manual work involved.