I don't know about using a cupcake tin and I dispose of my bags just because bags are usually a bad idea to keep parts in. I use small part organizers. You can purchase one at your local hardware store. They're available in several different styles; portable/stationary, plastic/metal, open/sealable. Take your pick to whatever fits your work environment. It's what I've used for over the past decade and I know right where all my hardware is.
- RCT