* Create devices representing your patch panels
* On each patch panel, create "rear ports" and "front ports" (in that order)
* Each front port that you create must be linked to a rear port: that's why you create the rear ports first.
* Multiple front ports can be associated with the same rear port, e.g. for MPO cables. This is a property that you set when creating the rear port. For example, if you have a 48-way patch panel, where all the ports are connected 1:1 to another 48-way patch panel, then you can create a single rear port (say called "R") with positions=48. Then you can associate 48 separate front ports linked to the same rear port.
* Create cable(s) to connect the rear port(s) of patch panels together
* Create cable(s) to connect from device interface to patch panel front port, and if necessary from one patch panel front port to another patch panel front port.
So in your example, there is a cable from SW1365 eth 1/48 to PP1375 front port 45; a cable from PP1375 rear port 45 to PP1377 rear port 45; and a cable from PP1377 front port 45 to RT1424 Te 0/1/0. When this is done, you'll find the interfaces are connected, and you can also trace the cable path.
If you decide to have 48 separate rear ports then you'll need 48 separate cables from the rear ports of one patch panel to the rear ports of another; write a little script to generate a CSV file of cables, and then import it. I prefer to label front ports "F45" and rear ports "R45" for clarity, although this isn't necessary (they could both be called "45").
Alternatively you can create a single rear port R with 48 positions, and front ports F[1-48] linked to R. Note that the syntax "F[1-48]" is valid for bulk creation of ports, and works whether you are linking to a single rear port, or 48 separate rear ports.
There is one major stumbling block, which is that Netbox can't model SFPs, and it can't model a single interface connecting to two fibres. As long as all your fibre connections are duplex, then you can consider a "fibre pair" as a single cable, and the problem goes away. Same if all your SFPs are bidi. But if you have a mixture of duplex and bidi SFPs, it becomes unworkable.