Most of my paper is already organized Roy G Biv; cs and pp combined. It's working for me. The only paper I've separated for theme is Christmas/winter. Mainly, that's because I have YET to complete my December Daily from 2012.
The only time I have an issue is when I'm digging through for the right pattern in X color.... only to see the flip side of my pp would have worked perfectly on another project if only I had seen it when I needed it! I was hoping to find a fix for that. Admittedly, I scanned the email at first, so I'll go back and read again. However, it's stopped me from sorting the paper I've acquired in the past couple months. I'm afraid I'll lose it again.
For now, I'll suck it up, re-read for this week and get going on sorting what's out.