The package manager does not have native handling of resources. It has been listed as a possible future direction from the beginning and is currently listed as an evolution idea. In the meantime, various workarounds exist out in the wild: Workspace, Mint, etc.
Source code targeting iOS, watchOS and tvOS can be handled by the package manager, but the Application at the top of the dependency tree must still be a separate Xcode project (though it can be left mostly empty). See here for instructions.
The situation has been steadily improving. For example, the recent acceptance of SE‐0236 provides the ability to declare platform version requirements in a manifest and it includes specifiers for iOS et. al.