Alright, my setup is a tad bit different than everyone else's, but it works just fine. I put AM in my awesome folder and the rest of the mods in my Packages folder. That being said, here are some screen shots of how it should all look when you are all done:
The resource.cfg file should contain this:
[indent]
Priority 900
PackedFile Awesome/*.package
PackedFile Awesome/*/*.package
PackedFile Awesome/*/*/*.package
PackedFile Awesome/*/*/*/*.package
PackedFile Awesome/*/*/*/*/*.package
Priority 800
PackedFile Override/*.package
PackedFile Override/*/*.package
PackedFile Override/*/*/*.package
PackedFile Override/*/*/*/*.package
PackedFile Override/*/*/*/*/*.package
Priority 700
DirectoryFiles Files/... autoupdate
PackedFile Packages/*.package
PackedFile Packages/*/*.package
PackedFile Packages/*/*/*.package
PackedFile Packages/*/*/*/*.package
PackedFile Packages/*/*/*/*/*.package
Priority 600
PackedFile Testing/*.package
PackedFile Testing/*/*.package
PackedFile Testing/*/*/*.package
PackedFile Testing/*/*/*/*.package
PackedFile Testing/*/*/*/*/*.package
[/indent]
If you set up your folders to look like what I have then you should be able to add mods to the Awesome, Override, Packages and/or Testing folders and they should work.