You don't indicate when you will be traveling. Thus, we can't advise you on the best fare options. The very easy way to do this is to buy your ticket from the Swiss either online at www.sbb.ch or at the ticket station. If you have a Swiss pass or card, just show it to the agent and they will make the adjustment. Your pass should be good to Domodossola, Italy. I've looked and the Swiss want 151CHF ($169) for this journey. If you have a pass or card, there will be some type of deduction. If you are using a day on your Flexipass, then you should only be paying for the trip from Domodossola to Rome as the Swiss see it. Unfortunately, they see it a bit higher than the Italians do.
Here's a second option if you have 90 days before you travel. For this option, buy Swiss transportation out to Spiez (Muerren/Interlaken Ost/Spiez). About an hour of travel. You certainly don't want to a day on your Flexpass for this one. Then, transfer to the EuroCity train going to Milan via Visp, Brig and Domodossola. You might have a train change somewhere along this journey but if your lucky, you change trains once in Milano Centrale. You purchase the train ticket from the Italians at www.trenitalia.com. I can see fares right now in August for 61Euro. The tickets are non-refundable but that's a really good price.
For what you are describing above, you may not need any type of Swiss pass or card unless you will be 1) traveling to the higher mountain tops and/or 2) you will be in Muerren for several days and you will be day-tripping out of there. You normally have to expect ticket fares to exceed about 240CHF before any kind of pass or card becomes cost effective. Zurich/Zermatt is 120CHF. Zermatt/Muerren is 97.20. Muerren/Spiez is 14.50CHF. You're close. If you expect to travel to the Jungfraujoch and/or the Schilthorn, you should consider either the Swiss Card or the Swiss 1/2-fare card. The Flexipass is not as useful in going to the Jungfraujoch or Schilthorn as you only get a 25% discount to these higher peaks. You get a 50% discount with either the Swiss Card or 1/2-fare card. For the Jungfraujoch alone, it's a $50 difference between 25% and 50%.
