Firstly glad your planning ahead like myself we will be in Arriving in Geneva in June 2017 and are planning a similar trip
in order to get the best responses from here you need to state more what your interests are are you an outdoor person so hikes, etc appeal
Do you like museums and how long you plan to stay in each area.
We are starting off in Geneva and staying in the YHA in Geneva we are then going to stay in Gruyeres as the Midsummer Festival is on and there is also the Chocolate museum and cheese museum near which can be combined with a walk through a wooden gorge is that's your kind of thing.
From Gruyeres we are going to go down to Montreux and depending on weather go to Rochers de Naye on the cog railway and walk down . This we are hoping to do with a combined walk along the promenade to Chilion Castle and take the boat back.
From Montreux we are then going to take the Golden Panorama Express to Luzern and explore the town. We are debating to stay longer there and do a cruise on the lake combined with a hike of the area.
From Luzern we are going to do the Rhine Falls and go up to Zurich depending on time either continue onto Innsbruck that day otherwise stay over in Zurich.
From Zurich we are going onto Salzburg for the week
All accommodation we are doing on a budget and have chosen to stay in a 4 bedded room in the YHA apart from Gruyeres which average between CHF 150 -180 a night and generally include breakfast which is a bonus. If this is your type of thing they are also a great way for your children to meet other nationalities
We debated which pass to use as we were originally going to get interail passes as this will cover a number of countries.
We have gone with the Swiss Rail Pass for 5 days as that is how long we are in the area. The reason being is that you can just hop on and off the train and are not restricted to set time. With the interail card you have to write down every journey you do once you get on the train which can be very time consuming and also some trains you do have to book seats for that way. it also only offered a max of 50% of some trips
Everything I have mentioned above is free with the Swiss Travel Pass and there was a big saving when I did the comparison use the excel spreadsheet in the section compare railcards just comparing a few things as nothing is ever set in stone so to speak but try to include everything you would like to do
As our final destination is Austria we are just going to buy a on the day ticket as most of our time we are just going to explore locally and will get the Salzburg pass to cover this.
Hope this helps