It should include sub folders if it's done correctly. I've seen people with problems like this before, but it was not the applications fault. This process is very similar to iTunes' import. Except you have the choise to skip files that you have deleted before, and the extention support is far superior.
- Go to File -> Library - Import Folder. Browse for the root folder of the music files
- Mark "Add this folder to auto-import list" if you don't want to run the import manually
- Choose Advanced and mark Audio so all sound files is added
- Loose the mark on "Ignore files previously removed..."
- Click import
If you're going back to iTunes because of a problem like this, then I feel sorry for all the good things you'll be missing out on. Well, they DO have the integrated iPhone support don't they? That's something...
Good luck with the import