To add a new transformer to the site, click on the 'Add Transformer' map tool (highlighted in red below):
A yellow popup menu appears allowing you to choose the transformer type to add (from your previously defined transformer specifications):
Then click on the map to add a transformer instance of the type you selected. No physical object (that shades modules, for example) is added to the site - it is just a placeholder for the transformer.
The transformer instances appear in a table in the Transformers tab in the lower pane of the screen: