How do I add or remove folders from an existing backup?

On the backup set's card, click Add folder or file to add something, or click the minus button beside a folder to remove it from the set.

Removing a folder only stops future backups of it. Versions already saved still contain it, so you can still restore its earlier contents from Versions….

Adding a folder means the next backup includes it. Because it's new to the set, that backup will be larger than usual — the same "first backup is the biggest" effect, just for that folder.