>> Also on a couple of them bumping up to 1st class from our 2nd class Swiss Travel Pass Flex would be a nice experience. I believe I can do that at the rail stations should it appear really crowded as well as following the great directions previously listed for the SBB app.
Buying a class upgrade from the ticket counter is always an option, but if your train is departing on one of the more distant platforms, you can't wait until it arrives before deciding on the upgrade, as you probably won't have time to get to the ticket office and back - and there may also be a queue. That is where the app comes in handy.
Thanks to rockoyster and others, I think we have now solved the difficulty of getting a class upgrade for the correct price (i.e. half price) in the SBB App if you have a 2nd Class Swiss Travel Pass.
I have just run through it on my SBB App, which is the version for the iPhone. During the purchase process, you get the option to "Edit travelers". Using this option, you can change your traveller status from 1/1 (full fare) to 1/2 (half fare), and then choose "Class upgrade (route-specific)" as your purchase option. Just remember to change it back to 1/1 if you need to buy any point-to-point tickets on days not covered by your Swiss Travel Pass!
>> So, one cannot purchase a seat reservation (not a ticket but just the reservation) on the SBB site?
Yes, if seat reservations are available on a particular train, you can purchase reservations on the SBB site at the page below. But note that on many regional trains, seat reservations are not possible.
There are also limits on how far ahead you can purchase a reservation:
> Online 60 days in advance
> Mobile app 30 days in advance
If reservations are possible on a particular train, 2nd class reservations will get you a guaranteed seat, but it can still be tricky to find somewhere convenient to stow your luggage. As 1st class is generally less crowded, stowing your luggage tends to be less of a problem. Doing an upgrade to first class is therefore my preferred option for dealing with a crowded train when I am travelling with luggage. Of course, reservations are much cheaper than a class upgrade!