If you look for paper by manufacturer, then sort it that way. The most important thing about the way your paper is sorted is that it works for you.
I generally sort mine by colors and by about two dozen themes, because that works for me, but I do have a few stacks I keep together. If a lot of your paper packs are themed, you could still sort by theme, and keep solid-color stacks separate. I have a food themed stack in the same slot as all my loose food themed paper, I have a zoo themed stack in the same slot as all my loose animal-themed paper.