Do you have Rick's Switzerland guidebook, which covers lots of sightseeing details for those areas? Remember also that the Tourist Information office will be a good resource for maps and activity pamphlets while you're there.
If you definitely want to include Lake Como, then it makes sense to fly home from Milan. Any route across the Alps between Switzerland and Italy includes some nice scenery, but the slower route via St. Moritz and Tirano is a popular option, a portion of the Bernina Express. Between Tirano-Varenna-Milan, you can get train schedules through the Swiss railway site (www.SBB.ch), but not through the German DB link that we use for other areas.
Let's say you spend 4 nights around Muerren and 3 nights at Varenna. That still leaves you a whole week to plan. The Bernina Express is not the only scenic train ride. If you head west from the Muerren/Interlaken area to Lausanne, then take the scenic Golden Pass route, via Zweisimmen and Montreux.
You'll probably want a Swiss Travel Pass, which covers trains, buses, boats, and museums, and gives 50% discounts on most mountain lifts (but only 25% off between Wengen and Jungfraujoch/Top of Europe). Your son travels free with you if you request the Swiss Family Card at the same time.
You could also make an appointment with out paid Trip Consultants. Many of their recommendations will be covered in the book, but they can help you plan it out on a calendar.