I use an over the arm sewing organizer, similar to a TV watcher's organizer that holds the multiple remotes. Mine is made from pre-quilted fabric. It has a pin cushion at the top, and two pockets on either side. When using it, the pin cushion is exposed, as well as the two pockets. When not using it, it folds up so that the pin cushion and pockets are not accessible.
I hold projects in the Zip-loc Big bags (XL size). If I need more thread than I can put in the sewing organizer, I might use a small ziploc bag.