For each new subfolder you want to add copy the last packed file line in Resource.cfg and a a /* to the line just before /*.package.
For example:
PackedFile Packages/*/*/*/*/*.package
And then add a /* like so
PackedFile Packages/*/*/*/*/*/*.package
Copy this back to your Resource.cfg file just under the last line in the group. This will allow the file to see one more folder deeper.
Here's an example photo: (Click to see larger view)
