If you have manuals for tools and equipment scattered throughout your shop, basement or garage, putting them all in one place will eliminate searches. You can commandeer a two-drawer file cabinet for your manual center, or else consider using an older suitcase. You should be able to find such suitcases in perfect shape for only a dollar or two at garage sales or swap meets, being sold by the owners because they are out of style. Even a smaller suitcase will hold dozens of manuals and can be stored either vertically or flat.
Just about all toolboxes have tote trays. Tote trays keep smaller tools and parts separate from larger ones. If a large percentage of your tool set is made up of smaller tools and pieces, perhaps it's time to look into getting a multi-drawer tool chest. Slightly larger than a toolbox, it allows you to divide and organize small tools into groups that can be quickly located, collected, and returned.