First of all, I suggest you not to buy mountain railway tickets in advance. Only buy them on the day of travel. In case the weather won’t be good you will have spent money for nothing.
The Swiss Travel Pass entitles free travel to inhabited places only. Any place above the inhabited places is not free of charge, with the only exception of Mt. Rigi, Mt. Stanserhorn, and Stoos.
When using cable cars, gondolas, or mountain railways simply buy the tickets from the ticket window or the the railway travel center and mention that you hold the STP. The staff will let you know if the STP is partially accounted or not.
What concerns the Jungfraujoch trip, the STP grants free travel to Wengen. From Wengen to Jungfraujoch you will have to pay 75%.
When looking for tickets there isn’t any possibility on sbb.ch to save the STP which is then taken into account by the webshop and offering discounted tickets according to the STP validity map.
If you allow a travel tip: if you are going to Mürren, there is a very nice spot called “Winteregg” (google for images); it’s a railway stop between Grütschalp and Mürren. You can walk from there to Mürren in about 40 minutes. In my opinion, Winteregg is one of the most beatuiful spots we have in Switzerland offering breathtaking views on Eiger, Mönch, and Jungfrau. And the food which is served at Winteregg restaurant is authentic swiss.