The short answer is that you can't. I'm not really sure why you'd need to do this, the files are uniquely named so a separate folder doesn't really seem necessary to me. Is there a specific reason you absolutely need these files to show up in separate folders? Can you not just move these files into the right folders after logging?
The long answer involves painfully scripting a bunch of events to basically re-implement the logging feature. You could also look at /savebuf and the window icon -> Buffer -> Save As... menu item, though these are probably not much help to you.
On a sidenote, you can separate logfiles into folders given by the network the logs came from, but that probably doesn't help you either.
