There are many plugins available for media management and file management which will allow you to specify where you want uploaded files to go based on user or other requirements.
https://www.google.com/?gfe_rd=ssl&ei=lY5zVprEJuSD8QeMkJ7gAw#q=wordpress+plugin+file+manager
https://www.google.com/?gfe_rd=ssl&ei=lY5zVprEJuSD8QeMkJ7gAw#q=wordpress+plugin+media+manager
There are also upload manager plugins:
https://www.google.com/?gfe_rd=ssl&ei=lY5zVprEJuSD8QeMkJ7gAw#q=wordpress+plugin+upload+manager