Nuts and bolts

My wife says I've lost it, but when I disassembled my 65 formula s I sorted the nuts and bolts by size. Now I'm putting things back together I noticed the bolts have different markings. I found the correct valve cover ones. These may not be correct, but some have 3 dots across the top. Some have a large circle with smaller circles inside.
I think I've watched to many episodes of graveyard cars. Thoughts

You should separate them according to application, not size....