First, are you using Tier 1 or Tier 2?
If you are using Tier 2, all input files start in a directory named 'media' (which is also where you put your bytecode.byc file). You need to add the media directory to the Resources folder in your Xcode project. Make sure that "Create folder references for any added folders" is ticked next to "Folders" in the dialog that pops up to select your media directory. This makes sure that any sub-directory names and structure are maintained and available to your app. Then select the media directory (not the files, but the actual directory the first time).
If you are using Tier 2, I would still recommend having a directory named media in your project (both Windows and Xcode) to keep the media separate and easy to identify. You would make sure to add "/media/" to file references.
Tier 1 looks specifically for a directory named 'media' by default. Tier 2 does not.
When you create or update a file by writing one, it creates the file in the appropriate sandbox area for the platform. In Windows it is Documents\AGK\<yourappname>\media (for Tier 1). Plus any subdirectory under media (Tier 1) or your main app (Tier 2). After the file is written there, if there is a file of the same name in <yourappexecdir>/media, the app will use the one in the sandbox area the next time it reads it. Other platforms create similar directories somewhere (usually hard to find).
Cheers,
Ancient Lady
AGK Community Tester