A lot of great suggestions here geeks. I think one of the reasons I get so conflicted on how I should do this is because I don't really have boxes of anything. Just a handful here and a handful there.
For now, I've decided to go by brands, with some variations. One of my small 50 counts is a glasstop and just does not hold humidity as well as everything else. That's where I've put my one-off singles I don't care about and the brands I don't mind giving away. The other two 50 counts hold my Alec Bradleys, 601s, Toranos, and the like. They're kind of my in between sticks that are worth more, smoke better, but yet still aren't my absolute favorites. My wineador, which holds excellent humidity, is now home to all of my Drew Estate, DPG/My Father, Oliva, and Padrons (as long as they are still in the cello). This is my "favorites" humidor. Lastly, my dome holds all of my Tats, AJ Fernandez stuff, and one-offs I do care about. The trays on top hold my un-celloed sticks. This humidor as a great aroma so I figured the nakeds belonged in there.