This can be a struggle for everyone I think. I have seen so many amazing scrap rooms and these amazing paper storage systems they have and I am sooooo jealous. Right now I have a small 6 shelf paper rack that I sort my pattern paper into. My stacks are pretty general (outdoor, holiday, seasonal, school, sports, pattern) since I don't have many slots. Some day I hope to have a much larger storage system so I can separate more.
When I go to crops and such I use these awesome plastic cases that expand and have a snap close lid. This way I can put everything in them that I need for that layout. I actually find myself filling these cases with all the supplies just to keep everything together, even if I'm not going to a crop or retreat any time soon.