So if I understand correctly I can include the necessary flags and argument for cross-compiling in a destination.json file?
If you're using the Swift package manager, yes, though I've never used that json cross-compilation config myself. I thought you wanted to use Xcode, so I just gave you the cross-compilation flags that would be needed either way.
Can I have multiple destination.json files one for macOS and one for Linux?
You pass it in with a --destination flag, so that should work.