I have done it both ways, just depends when I need to pot daylilies. Like you in 2006 I saw rust for the first time and have never seen it that bad since, I have worse problems with spider mites than rust. I do spray for rust, and still always get a little in the fall, but not enough to get excited about.
Good luck with your raised bed, you can use any kind of potting "mix" or compost. I would not use potting soil or dirt, because both will become compacted and not drain very well.
