When we have out of town visitors, we do the 49 mile drive in San Francisco as an easy to follow way to hit all the tourist spots. It's a marked tour and you can follow the signs around the city or get a brochure from the visitor's center, but there is a handy guide book that is nice to have for a little more information on the various sights. We can easily do a quick overview of the city in a day, or more depth in 2 days. This isn't going through museums, but we do generally get out and explore a little in various places like Fisherman's Wharf, Golden Gate Park, etc.
I also would suggest the Bay Area Discovery Museum for the kids, right across the Golden Gate Bridge in Sausalito. The view is magnificent, it's lots of fun for their ages, and it's in an old fort so the architecture is interesting, too.
The Jelly Belly factory is in Fairfield, about an hour outside of San Francisco without traffic. It's about 20 minutes from Napa, though, so if you wanted to add it to that day, it could work. There isn't much else out there for kids and having done the tour, I wouldn't go out of my way for it if you're not already in that area. Take I-80 out to Fairfield and then HWY 12 up to Napa.
If you are driving up, take the Pacific Coast Highway. The scenery is lovely and it's a far more interesting drive than the 5.