I am trying to hide 2 secrets that I am using in one of my apps.
As I understand the keychain is a good place but I can not add them before I submit the app.
DO NOT store an S3 key used for write in your app! In short order someone sniffing traffic will see the write call to S3, in shorter order they will find that key and do whatever they like.
The ONLY way an application can write content to S3 with any degree of security is by going through a server you control.
If it's a key used for read-only use, meaning your S3 cannot be read publicly but the key can be used for read-only access with no ability to write, then you could embed it in the application but anyone wanting to can pull it out.
To lightly obscure pre-loaded sensitive data you could encrypt it in a file and the app can read it in to memory and decrypt before storing in the keychain. Again, someone will be able to get to these keys so it better not matter much if they can.
Edit:
Based on new information you are probably better off just embedding the secrets in code. Using a tool like iExplorer a causal user can easily get to a core data database or anything else in your application bundle, but object files are somewhat encrypted. If they have a jailbroken device they can easily get the un-encrypted versions but it still can be hard to find meaningful strings, perhaps store them in two parts and re-assemble in code.
Again it will not stop a determined hacker but it's enough to keep most people out.
You might want to also add some code that would attempt to ask your server if there's any override secrets it can download. That way if the secrets are leaked you could quickly react to it by changing the secrets used for your app, while shutting out anyone using a copied secret. To start with there would be no override to download. You don't want to have to wait for an application update to be able to use new keys.