Are both your kids really excited about animals? Their enthusiasm is going to play a lot into how you get around the San Diego Zoo, how long you stay, and which order you do things in.
If you want to see the whole park (a mammoth undertaking to be sure) I recommend something like this...
Get there early (at opening!) and watch the bird "flyover". Walk immediately to your right and go through Australia (Tasmanian Devils, Koalas, Wombats), then circle the Urban Jungle -maybe in time for giraffe feeding! (giraffes, rhinos, cheetahs, a few exotic cats and birds). From there, continue on the main path around the camels and birds and stay on the high ground through to Elephant Odyssey. This area has a LOT of interactive children's activities, so if your kids are into that kind of thing this is where they'll get to play a bit. If you walk all the way through that exhibit you'll end up by the mountain lions and maned wolves facing the skyfari tram. At this point a rest might be nice, so take the skyfari back to the front of the zoo. Immediately exiting the skyfari is the reptile house and reptile walk, and that's very well shaded as well (a nice place to hangout if it's hot out). After going through that, keep going straight (past the stadium) and you'll end up at the hummingbird house and children's zoo - which is another great interactive area for the kids. From there, tackle the gargantuan interior of the zoo ("Lost Forest") - there are multiple trails to take here that will take you past the Orangutans, Gorillas, Bonobos, Tigers, Hippos, and all kinds of other charismatic animals. All the trails eventually run back into each other, so look at a map and plan according to the animals you want to see most. If you finish up back at the top, you can walk down the hill and see the bears through the "sun bear tropics" area as you go back into the canyon. Immediately at the bottom of that trail is where the pandas are.
I know the conventional wisdom is to see the panda's early to avoid the queue - but in the summer you're likely going to have to wait no matter what and the zoo has set up a really nice area (with red pandas, snakes, and Takins) to view other animals while you wait to see the giant pandas - this will also be one of the most memorable things at the zoo for you, so doing it next to last I think helps to build up the excitement.
From there, you can continue to take the outside path towards the skyfari tram in the back of the zoo and see the Arctic Area (Polar Bears, Arctic Fox, Caribou) before riding the skyfari back to the front of the zoo again to go home.
That's an all day event. Just a suggestion.