Quick question about uploads
 

Should there be files in the uploads directorys. I thought everything was stored in the data directorys? Can / should I clean them out every now and then?

There should be no files in the uploads directory only unprocessed files. You can delete anything under uploads as it has not been uploaded yet to your gallery. Either a user left before processing it or they where having problem getting your site to process the file I would think.

So all the folders and files under uploads are ok to delete and it will start from scratch the next time a file is uploaded?

Yes that is correct uploads is merely a catch all directory for user uploads before the system processes them.