This will make a lot more sense in you look at a map of Swiss rail lines, here: https://www.sbb.ch/content/dam/infrastruktur/trafimage/karten/karte-sts-pass-gueltigkeit.pdf
"Where do you fly into?", "What is the best way of doing this?" - Fly to Zürich, then get a train immediately to Luzern (70 minutes from the airport station), which is where the Golden Pass route starts. Spend at least one night there.
Golden Pass route:: Luzern - Meiringen - Interlaken - Zweisimmen - Montreux (see map). Possibly split this, and stay at least one night in the Jungfrau region, which is the area south of Interlaken, as you can see from the map this is accessible by rail. Probably 1 night in Montreux.
Glacier Express route: Zermatt - Visp - Brig - Andermatt - Disentis - Chur. Stay at least one night.
You are now in the south-east, and need to get south to Milan to catch a train to Vienna. Lucky Chur is also the start of the:
Bernina Express route: Chur - Pontresina - Tirano, the only route to Italy that goes over the top of the Alps. Notice the serious amount of squiggly pigs-tail loops on this route.
From Tirano you can catch an Italian train south to Milan, and another from there to Venice.
You need to build some more overnight stops into this.
"Should I reserve on both now?" - One important thing you need to know about Swiss trains, ALL routes (all the red lines on the map) have at least one train an hour. The named tourist trains are extra trains, that run once or twice a day, but you have lots of other trains to choose from. You only need to reserve these extra tourist trains.
For Swiss train times see the SBB (Swiss Federal Railways) website: https://www.sbb.ch/en
"Is getting a Euro Pass worth it?" - NO. For Switzerland, for this amount of travel, what you probably want is a Swiss Pass. see here: https://www.sbb.ch/en/leisure-holidays/travel-in-switzerland/international-guests/swiss-travel-pass.html
The only extra charge will then be the reservation fees, if you decide to go on the actual named trains.
Italian trains are so cheap, a pass is never worth it. You will get serious discounts by buying your Milan-Venice ticket in advance. Go to the Trenitalia (Italian Railways) site: http://www.trenitalia.com/tcom-en