There are two parts to the solution. The first part is to create and set the boolean. To do this, you need to create a variable, probably in StationGlobals so that you share between your process model and client sequence file. You could also put the variable in your process model file, but the property path is not quite as obvious. To set the variable, you need to add the PreUUT callback to your client sequence file. Then you can replace the serial number prompt with your own code (we used LabVIEW), including a check box for your boolean. Alternatively, you could use the existing serial number prompt and add a second step for setting the boolean, but that is more cumbersome for your users.
The second part is to implement the proper stop/run behavior for your
steps. This is done be specifying a custom post action for each step. To do this, I recommend that you define a custom step type. That way you don't have to edit this for every step. Once you create the custom step (probably based on the standard TestStand step types) edit the properties and select the Default Post Actions tab.