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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.