It is always a pain in the butt to try and remember where the long & short bolts are installed, when I have pulled the side cases or any other items off my bike, especially after a couple of days (or weeks) between work sessions. Here are few ways you can keep track of where each bolt goes.
First remove the bolts one by one. Then lay the bolts out around the item as they came out of the case/item. Get out the camera & take a photo of the item with all the bolts layed out around the item in the exact place where they were removed from. You then have a permanent picture that you can refer to at any time in the future.
After that get a ziplock sandwich bag, write the name of the item removed on the front of it & store the bolts in it so I dont lose them. I then stack the bags in the order that I removed the items, for easy reassembly.
TIP : Use a light coloured surface, to lay the bolts out, for good contrast.
Leave your nuts at home
Every time you take off a part hand thread the bolt or nut back in its home....you can tear a bike to the floor and put it entirely back together without spending 1 extra minute of your life than you need to looking for nuts and bolts all over the shop, and even better, remembering two weeks later which bolt went where can be tough even for a pro. if they are in their home holes they never get scattered, and you never gotta go and stick a home depot bolt in your bike.....I hope this saves you hours of frustration.
Alright here's a pretty easy solution to keeping track of your bolts. Take a sheet of cardboard, and put holes through out. Now when you take bolts off, label on the cardboard to were it goes. Then put the bolt in the hole.
Magnetic Parts Trays
Another trick is to arrange the bolts in order in a magnetic parts tray. If you are pulling a case cover, put them in a circle around the edge of the tray, leaving a space to remind you where you started. Keep several trays, and use one for each sub-assembly that you take apart. These trays are pretty cheap at Harbor Freight.