I never worry about keeping them in order, just pile them.
when reinstalling just place them in holes, don't turn them, they will all stick up about the same length (1/4 inch or so) over the top of the holes if they're in the right place.
If one sticks up way high, there will be one sticking all the way in, so swap them about.
very seldom will you find bolts that stick up hgher than the others in the same application unless they are larger bolts, and then the larger diameter is the guide.
Ken.
Edit:
A while ago I built a 2.3 turbo, after the build I had it sitting in the garage while I worked on the car for it, so I placed rags in the intake/exhaust ports to keep crud and dust out of it. when I got ready to install it my 5yr old daughter was in the garage helping, got the tranny in while she was playing around with the motor, got ready to put the motor in went to pull the rags and didn't see them looked on the floor and Kendra was playing with the rags, no problem, so I install the upper manifold, hook everything up and start it up. and nothing, played around with it for a bit, and it would just turn over not start, it's got fuel, and I can hear the injectors clicking, so I start digging around, pull the intake back off and find that she had stuffed the rags as deep as she could into the intake ports and must have picked up other rags she was playing with. thought the valves would be toast because I had to take the entire intake off and rotate the motor around to get the rags out of the valves. turn it a bit, pull on the rags, took longer to get the rags out than it did to install the motor and trans in the first place.
Ken.