And yes, you can create subfolders--the Clip will find the music, etc. regardless.
One thing: files put in the Podcasts and Audiobooks folders can be treated differently by the Clip--most specifically, the Clip can use the files' file and folder names for database display purposes instead of relying on ID3 tag info. which you otherwise might need to fill in. If you would like the benefit of that, you should keep and use those folders (or, the same effect can be obtained if the files' ID3 genre field is set to audiobook or podcast, regardless of folder location).