The link about rail passes here in My Swiss Alps has an expandable *.PDF map that lets you see what each pass covers...free, discounted, etc.
In the Jungfrau region, an STP covers the trains or cable cars as far as Mürren or Wengen, and, on the other side, as far as Grindelwald. These are population centers and as such are accessed by public transport (or by private rail services subsidized by the government(s)).
Above Mürren, above and beyond Wengen or Grindelwald to Kleine Scheidegg, or from Mürren up to Schilthorn, the STP provides a discount, if I recall correctly. I think it is 50%. Those are privately run excursion lines, which also are called mountain railways.
Please note that in the timetable, the fares that first appear for regular train trips (etc.) on public transportation are already discounted by 50%, because essentially all Swiss have 50% discount card.
If you work your way further into the menus, as if you were actually going to buy a ticket, there will appear a place where you tell the computer what kind of pass you have, if any. At that point, the actual fare is calculated. Rule of thumb- if you have no rail pass of any kind, double the fares that first show in the timetable on regular (non-excursion) routes. I know that is not simple or clear, but that is how the system works.
Check the validity map I mentioned, or wait for Arno or Annika to jump in. That will show the no-fare and discounted fare lines.
I'm sorry that I cannot be more clear, but I never use those passes ( I have a Half Fare Card) so i don't keep up on the details.