Have an assembly strategy, such as:
http://www.restorick.com/tech/forum.asp?FORUM_ID=20Set up a spread sheet to organize your numbered bags and numbered boxes.
I organized the spread sheet first by areas of the car: engine bay, front, interior, interior-front, interior-instrument panel, interior-rear, rear, side, trunk, and under. Then by numbers of the chapters of the Service Manual that apply. That is, 01 is Accessories, 02 is Front Suspension, 03 is Rear Axle, 05 is Brakes, etc.
The spreadsheet is put together randomly, then sorted by area then by chapter.
If I want to work on the rear axle and the rear springs, I go to the spreadsheet > Under > 03 Rear Axle and 17 Rear Springs. Here are listed by numbers all the zip lock bags and boxes that apply to these items.
All zip lock bags are stored in trays (actually box lids) and in numerical order. All boxes are stored in numerical order.
I can retreive any bag or box I need quickly.
