I agree with everything Dan said.
I sometimes wrap some tape around the inner cable before I cut it. That reduces the chance that it frays.
I prefer the Sram cable cutters. They work well on shift and brake cables, as well as outer housing. I checked, SJS does not sell it with the SRAM logo, but it looks like this one with a different name on it. Mine (Sram) has red handle, not yellow. The awl in the handle is great for making sure the end of an outer housing hole functions well after cutting it.
www.sjscycles.co.uk/tools/jagwire-pro-housing-cutter/But SJS also have much cheaper cable cutters too.
I assume you are aware that Rohloff shifter cables use brake outer housing that is NOT compressionless outer housing. No need to use the compressionless shifter housing that is sold for derailleur bikes.
I do not know why your frame would have two sets of cable stops on the downtube for a frame built for a Rohloff. Perhaps the frame builder did not realize that Rohloff cables have to have some slack, that there is no reason to use bare cable along the downtube. But for aesthetics, do it any way you want.
I have started using Dan's suggestion for superglue on the end of the cable to reduce fraying, that was a great idea. But it has to harden before you use it, you do not want to accidently glue the cable tip to something.
If you use your bike for touring, it would be a good idea to make sure that both cables are exactly the same length, and cut a third cable to that length too in case you needed to replace a cable later on a tour. If you already have a cable cut to correct length, it simplifies cable replacement. That means that the outer housing length for both cables should be exactly the same too.
I see PH made some comments while I was writing mine, I agree with everything he said.