Assuming Tier 1, you would have a directory named media. And you would make any sub directories under that.
I'm now working in Tier 2, having converted my Tier 1 project. And I kept the media directory for simplicity. And it does.
For accessing (read or write) files, I add '/media/' ahead of any file name. This works very well on all the platforms I've tested it on (Windows, iOS 5.1/6.0 and Android 3.2/4.0).
And the AppGameKit engine will create the directories and files specified, when you write stuff, in the app's work area (most platforms sand box apps).
If you avoid using the SetFolder and SetDirectory commands and just explicitly add the path to file references, you should be okay.
Cheers,
Ancient Lady
AGK Community Tester