Tomorrow I am flying from Geneva to Prague with a layover in Zurich, all operated by Swiss. I should land in Zurich at 16:40, probably at the terminal 1 (since it is a domestic flight). My connecting flight to Prague is either from terminal 1 or 3 (that is what check-in says) and the boarding starts at 17:30. Can I be sure that I will not to miss my flight, assuming everything will be on time? In other words, is terminal 3 close to terminal 1? I found only that the terminals at Zurich airport are A, B/D and E. So I hope that terminal 1 is A and terminal 3 is D, maybe? Thanks!
You're misunderstanding it, there's only one terminal at Zurich, but with different gate areas (A, B, D and E), of which A and B are used for Schengen flights (such as to/from Geneva or Prague), and three check-in areas for departing passengers (1, 2 and 3), which is irrelevant to you since you're connecting.
You'll be arriving either in the A or B area, and then follow the transfer signs to the appropriate area, depending on where the departures Monitor tells you to go. Most Swiss flights leave from an A gate.
Regardless, you should be fine unless the flight from Geneva is delayed. Worst case, Swiss has to put you on the next one for free.