I have several big shoe boxes and they are marked with name of project on the sides, so when I am ready to work on them I can just pull out the shoe box that I want. I can stack them, when I say big shoe boxes I mean like boots and big boy shoes .haha.
When I moved things into this room several years ago, I designated a place for everything so when I need to clean up after a project, I know where everything is supposed to go and it eventually does. I have two sets of plastic drawers that have 2 thin and 2 deep that keep all of my tools and have slotted wooden tray on my table for my rulers..always within reach. Small spools of thread go in a plastic 2 sided partitioned case and cone threads in the deep drawers.
All my fabric are folded more or less by color, children, holiday, flannel, ethnic, 30's, etc.