With kids those ages, I would recommend the Reuben H Fleet Science Center and the San Diego Natural History Museum. The San Diego Air and Space Museum was really neat too, and I enjoyed the Museum of Man, but I think those museums might be a bit too much work for a 6 and 9 year old. We went to the Aviation museum last year when my boys were 10 and 12, and the 10 year old got tired of it long before the rest of us.
You could do the two science museums I suggested and the model railroad museum in a day and still have time to eat lunch and walk around the grounds a bit. I would recommend getting to Balboa Park before 10 AM so you can get a full day out of the experience (plus parking will be a breeze). The museums will open at 10 AM, and most close at 5 PM.
I really like Balboa Park. The first time we went, my boys were 3 and 5 and loved the Fleet Science Center. We spent at least half a day at the museum then had our picnic lunch and strolled around the grounds. We finally made it back to San Diego last year (boys 10 and 12) and did 1 1/2 days at Balboa. We saw the science museum, natural history museum, and Museum of Man on the first day. Then we did the aviation museum on the second day, spending nearly 3 hours there before going off to explore other parts of the city. This year we did one big day at Balboa Park and decided to get a little bit of everything. We visited the Fleet Science Center, natural history museum, Museum of Man, International Museum, San Diego Art Museum, model railroad museum, and San Diego History Center, staying 30-75 minutes at each depending on our interest level. It was a full day! What was nice about that experience is that we got to see a variety of exhibits and learn lots of little tidbits about an assortment of topics, but we never stayed in any one museum long enough for my 11 year old to start complaining.