So, you’re earlier questions about photo mapping individual papers? The answer is obvious when you integrate with the digital library methodology. Of course, all individual sheets of paper must be aggregated into larger bundles, such as reams of 500 sheets. Now, placing that into the photo map is easy. The same principle can be extended to smaller objects too, that they must be contained within some kind of larger case together.
On the other side of affairs, in the scan to digital library world, you want small objects to be aggregated together into larger objects, but not too large all at once. Papers should be packaged into reams of no more than 500, then the reams can be placed on shelves or in boxes for larger scale aggregation.
Finally, this rule extends to all other small objects too. Just like a ream of 500 sheets of paper, every small object should be solidly held in place so that they retain an “address” that can be consistently navigated to. No bags where things can swish around and require searching are allowed. So yes, this does mean that you should create one of those nifty cases that has styrofoam filling up the space in the case, and cut-outs in the shape of each tool that fits securely in its place. It’s not just an eccentric overly-organized way of doing things. After all, once you create the cut-out where each hole is in the shape of each tool, you can assign numbers next to the holes.