There is no such thing as a Primary and a Secondary Apple ID. If you have two Apple IDs, then the purchases made with either ID will be tied to that ID forever. The iCloud information that goes with a given Apple ID also "belongs" to that Apple/iCloud ID.
You can start using the other ID, but you will still need to make sure that any iTunes library that you are syncing with on a computer is authorized for both IDs in order to be able to download and play purchases from both. You will also need to know the password of both in order to update apps on your device.
The iCloud information stays with the Apple/iCloud account. You can sign out of iCloud and keep the Contacts for that iCloud account on the iOS device, and then merge them into another iCloud account, but Calendars, Notes, etc. remain with the iCloud account that they were created under.
Does that clear up your question?
Cheers,
GB