Hello Bazthewaz
The how to use a Saver Day Pass, and how to book a particular train/seat while holding the Saver Day Pass, are very frequent questions.
May I refer to this thread in which, I think, I also have answered your questions:
https://community.sbb.ch/d/22713-how-to-select-train-time-and-seat-with-saver-day-pass/2
I can assure you, using the Saver Day Pass is the most easiest thing. Once you get the hang you might come to that conclusion, too š
Also, our SBB Community, together with @Sarah_W, we are about to improve the information on the use of Saver Day Passes. It is needed, your question is great evidence.
Get back to us if we can assist you any further.
Btw, the reservation for the Bernina Express you have done correctly; now you simply have to grab your STP and hop on that train š In my opinion, it is the most picturesque and diverse train ride our country has to offer - enjoy it.
Kind regards,
Roland