Hi Edward,
If you're dealing with repeating structure, those optional sections should be added to the repeating group where they belong, so yes you'd have to move them. To avoid controls being added to the bottom of the data source tree and having to move them, before adding the control, select the node in the tree where you want to place your new field/group.
If there are no repeating groups involved then you'd only want to organize your data source into a hierarchical structure just so it's, well - organized. It's best practice to organize your schema after all - it makes your form easier to work with, understand, and maintain.
Cheers!