I noticed each time I send an audio clip to Audition CS5.5, PP 5.5 writes a render and replace audio file in the same folder as my Premiere Project. While this seems logical, it gets really really messy after the 3rd revision of the 20th clips.
Any tips for keeping Premiere projects well organized in the OS?
You can change this in the scratch disk settings. As to what to change it to, that's entirely up to you.