A lot of great advice by everyone! The only thing I will add is using pieces of cardboard to hold bolts. The baggies work great but there are time when you need certian bolts in certain holes. What I do is draw a picture of the part on the cardboard then punch holes for the bolts and put them in the holes. This works great for theings like water pump bolts or a/c brackets and anything else that has different size/length bolts holding it down.
Good Luck, Woody