You can do that, but those actions (the adding of the actors into the world and positioning them) will not be saved in your code unless you 'Save the World' after adding and positioning them. From the menubar, 'Controls>Save the World' will create the code for the actions you took. The scenario must have been compiled beforehand and no act cycles can be run before saving.

It should only take a split second (after you manually add and position your actors into the world) after making the two clicks -- one on the 'Controls' tab of the menubar and the other on the 'Save the World' selection of the drop-down menu.