Help with booking train tickets

Munich is a good daytrip from Salzburg, but not from Zurich, so I assume that's what you meant. For ticket purchase as you go, you would be looking at these approximate cost for your longer travel days, drawn from our Rail Time & Cost map.
Zurich-Salzburg (via Innsbruck) $125
Salzburg-Venice $95
Venice-CT $85
Florence-Naples $110
Naples-Rome $55
Total $470 in 2nd class
This total will be less if you're ready to lock travel in some dates and times now, especially for the overnight train. See links from http://www.ricksteves.com/travel-tips/transportation/trains/buying-tickets#advance-purchase.

You could also cover the above trips with a 1st-class Select Saverpass for 5 days of travel in 4 countries for $491 per person, plus about $45 for Italian seat reservation fees. Since this is not cheaper, the main benefit it offers is the option to travel in 1st class. (We think 2nd class is fine.) The sleeper reservation fee is extra with either tickets or a railpass.

Thanks! We aren't staying in Zurich...it's closer to the Lichtenstein boarder...

So if I'm ready to purchase tickets now which site would you suggest using?

For Italy, use http://www.trenitalia.com/cms/v/index.jsp?vgnextoid=4ddd1a035296f310VgnVCM1000005817f90aRCRD

Notify your credit card company first

Register on the site

Use Italian spelling for the cities Venezia S.Lucia, Firenze SM Novella

Looks like a great trip!

If you have troubles with your CC, Paypal is a good alternative. Use the local sites to pruchase tickets. So for your Swiss segments, use sbb.ch, for Italian use trenitalia.com. Like others have said, if you are willing to lock in to certain times/days, buy your tickets now and you will save a lot. Do note that Munich and Salzburg are pretty far for day trips. You may spend more time traveling to get there than you would spend seeing the cities. You might want to consider closer destinations for day trips.

Point to point is almost always better for Italy. You will want to purchase most of your longer trips (the ones that would use the faster trains - IC and Freccia trains) in advance because you will get a better price. You won't save anything on Regionale or Regionale Veloce trains, however, so feel free to purchase those upon arrival.

First thing to do on the Trenitalia site is click the teensy British flag icon to translate the page. Then you need to use the Italian place names. Also note that the calendar starts on Monday, not Sunday, and the date is entered day/month/year.

Thanks everyone! I guess I should clarify that we are spending one day in Salzburg and taking a night train to Venice.

I really appreciate all the suggestions!