The reference images folder is purely for your reference when downloading the example, but the SDK is not using that folder at all. In other words, it is a handy folder to get you started much faster and be able to point at them and recognize them right away.
In order to use your own images, you need to have an on-device collection in CraftAR and then download the corresponding bundle to add them to your project.
Please follow the steps described in the tutorial Create collection bundles in the CraftAR service (http://support.catchoom.com/customer/portal/articles/2019131-tutorial-create-collection-bundles-in-the-craftar-service) and then Manage Collection Bundles with the On-device Image Recognition SDK for iOS (http://support.catchoom.com/customer/portal/articles/2018671-tutorial-manage-collection-bundles-with-the-on-device-image-recognition-sdk-for-ios).
Let us know if you have any trouble following those first two steps.