It seems that when i upload media files through either the front or back end interface, they don't go to the correct folder. I have my server set up as "www.server.com/bs", and then folders for "2008" and "2009", but when I upload through the interface, it sends files to "www.server.com/2009", not "www.server.com/bs/2009"

Any suggestions?

Try this combination:

Server: www.server.com
Folder: /bs/2009/

It's important that the folder have a forward slash before and after

Great! Thanks!