iCloud is for storing the user's Document. So if your app is mainly about creating and handling Documents, iCloud will work fine. And these documents are for this user only. They will sync across the user's devices, but won't be available for any other user.
CloudKit is essentially a cloud database, where you can store structured data and related assets in the cloud. There is a public data store that is available to all users of your app, so that data can be shared between users (up to you who sees what). The public data storage of CloudKit does not count towards a user's iCloud storage limit.
So if you're just looking to let users sync their documents between devices, use iCloud. If you're looking to have data shared between users, use CloudKit.