You can manage the complexity of large .transform files by adding comment text to:
•The Comment field of Note items. These are added to the Center pane by right clicking and selecting the Note sub-menu. You can choose the Arrow direction and a Color. If you right click on an existing item, you can choose to place the Note automatically, above, to the right, below or to the left. Just start typing with the Note selected to append to the Comment field. The comment will be shown as a tooltip when you hover over the Note item.
•The Comment tab of Input, Transform or Output items. Check View>Show Comments to show these comments in the Center pane. The comment will be shown as a tooltip when you hover over the item.
•In the Notes window that is displayed when you select File>Notes... from the main menu.
You can also visually group related items in the Center pane to show that they are related.