Typically you diagram network connections, and then make good use of labeling the physical patch panel and cables. The reason for this is patch panels are only a physical pass through, If you are troubleshooting at that point, then you should be looking at it in person.
Here is a good link for some network diagrams link
I would diagram out the network from a layer2/3 perspective and go through the patch panels and physically label everything including the patch panel and the cables.