At the KBI we use a three column comparison table in a Word document.
In the first column we list all of the comparisons performed (i.e Item 1 vs. Test 1.1.1), in the second column we list the conclusions that we reached (i.e ID BFM, ID FPI) we have symbols for ID, ELIM, and INC, then in the final column we include a description of the conclusion we reached for each area (i.e Strong agreement of striated individual detail within the FPAS, correspondence exhibited on both sides of the FPI, agreement is of sufficient quantity and quality for identification).
Multiple tables are used for "group" of comparison examined. If we had three firearms each firearm would have a table that listed the comparisons of Test to Test and any ID comparisons. Then a separate table would be used for eliminations. Cartridge cases and bullets also get separate tables. We found this is an easy way of visualizing how the case ultimately breaks down. Currently we do not compare known samples to other known samples outside of training.
Hope this helps, if it is clear as mud let me know and I can provide further info.