On The Sbb Website, the prices you see are the half fare prices (it assumes you have the half card). So if you are searching train tickets on there and you see 50 CHF, its actually 100 CHF. So just keep that in mind when looking at cost. Yes I would utilize your BO card to make the fare cheaper.
You can go to Google Maps, and look under the train icon. You can adjust the date and time of your departure and locations up to 90 days, it will show you the scheduled trains and buses and the platforms and connections they have. You can use this to assist you in planning the route. as its faster than SBB website
Example say you traveling Wed Aug 21st Lauterbrunned to Lyon at 8am
The first train option departs at 8:21 to Bern (Free with BO Pass), the train arrives in Bern 9:52Am
Now search in google maps with train icon, Bern to Lyon 10am departure time and you can decide what time works best for you and THEN search on the SBB website to actually purchase ticket in advance OR!!! Based on what I can see trains depart Bern to Geneva around 1030am and 11am, so you will also have enough time to purchase from the Kiosk in Bern a ticket right then and there, if you are nervous about booking in advance and missing your connection.