Uploading files in a webapp can be extremely tricky and sometimes the quickest way to do it is to store the file directly in the webserver or into a DNS (like Amazon S3) and then to save the link and the metadata inside a table in the DB. The thing is that you'll have to deal with file permissions, server storage, file management and so on (which is perfectly fine, by the way).
I have two tables called hospitals and departments. I have a junction table between them which holds the departments in each hospital. But sometimes I need a list of "All hospitals with All possible departments" - regardless of whether they are linked in the junction table or not.