Hello,
cred tool doesn't support subfolders in an archive; so you must pack your files in one or more 'flat' archives (packages). Look at the demo#3 sources, for example. It includes 3 packages: one with logo images, one with level file in plain text format and another one with the rest (models, shaders, compiled level and so on). You can plan your packages in different way: split files by game levels, for example; or you can make one big package.