Hopefully you'll get some responses from some of the cyclists closer to Zurich regarding the trams and boats in that region. As for the SBB trains, though, the day pass for bicycles from the SBB is valid on all their trains, just look out for a bicycle logo on the door to tell you where to get on.
On the older trains, there is usually a bicycle symbol at one end of each carriage, where you'll find a place for bicycles with hooks up high that you hang the bike on using the front wheel. There aren't as many places on the newer trains. On the bi-level (aka double-decker) trains, the only place is at the opposite end of the train from the engine - half of the bottom of the carriage is devoted to a big bike rack. For the ICN trains (i.e., the white, tilting trains), you need a reservation for a bicycle costing an additional 5 francs (on top of the 10 franc day pass) between March 21st and October 31st, outside of those dates the reservation is not required. On the ICN trains, the bike rack is behind each driver's cab - so there is one at each end of the train and two more in the middle if it is a double-length ICN (i.e., two 7-carriage ICN train-sets joined together).
There are some
trains in Switzerland on which bicycles are not allowed, but not very many. Generally, these are on a few of the smaller train lines that are not run by the SBB, some of the special tourist trains, and the high speed trains from neighboring countries. The TGVs from France, the Cisalpino trains from Italy, and the ICE trains from Germany all have their own restrictions, which I do not know very well. To check that a certain train does allow bicycles, you can check the schedule on the SBB website
and if a train has a bicycle symbol with a line through it then you know that bikes are not allowed. You can also check this at the station by looking at the departures poster (the yellow poster that says 'departures' or 'abfahrt' at the top), find your train, and check that it does not have a crossed-out bicycle symbol on it.