Hi uknowwhichoo -
You picked an excellent time of year to visit the Alps. September is, on average, the driest month, so you have abetter chance to have good visibility. That iis our favorite time to go. In 2009, we were up at Männlichen, near the Jungfrau in late Septembe and had truly wonderful weather, See attached images:
The planning page linked by Annika is very thorough and includes a link to the timetable.
Even if you don't need all of the ideas in that link, simply using the timetable can often answer basic questions....for instance...how to get from any Swiss station to Paris.
I have attached a screen grab to show you an example from Chur.
If you open the timetable and find a journey, you can click on the "+" sign to the left of the particular journey to expand the details. In the footnotes of that expanded link, you can find a map of the journey.
Annika gave you the link for the Golden Pass route
The link for the Glacier Express can tell you where it starts and ends, and you can see where to get off or pick it up partway along the journey if you choose.
When planning journeys in Switzerland, I find a good map to be very useful. if you zoom in on this one, you can see the rail lines. if you use the menu under "Points of Interest" you can make the train stations visible, best done when zoomed in on the map a bit.
Annikas suggestion to focus on the Jungfrau region and take the Golden Pass route to Montreux seems to me to be an excellent way to meet your objectives.