Lived in the Los Angeles area for several years. You may want to divide up your trip and stay at different hotels for different parts.
Disneyland is in Anaheim, which is not remotely close to anything. If you're going to go more than one day there, stay nearby at a motel near the Anaheim convention center (if you want to stay cheap) or within the resort.
Hollywood is approx an hour away without traffic. To be close to Hollywood and Universal, I would strongly suggest staying in one of the hotels next to Universal (they have several, including a Hilton). You can then take the red line subway into Hollywood and walk around the more touristy attractions. The red line subway will also take you directly downtown to see places like the Disney concert hall, Parker Center, etc.
Universal City is in the San Fernando Valley, as are many of the studios (Disney, Universal, Warner Bros) and WB & Universal have backlot tours you can take. The Tonight Show is filmed at NBC in Burbank, but you probably don't want to take kids there. Burbank and Universal City are right next to each other.
For another part of your stay, you'll want to see the ocean, and you want to get to Santa Monica. They have an outdoor shopping mall (the 3rd Street Promenade) that isn't anything you haven't seen here, but it's nice. There is also a tiny amusement-park-thing on the Santa Monica pier with a ferris wheel.
I hope you are renting a car. I'm telling you about the red line because there is NO parking in Hollywood or downtown (you'd pay an arm and a leg for it) but the train is quick and easy. Unfortunately, the train only goes to a limited number of worthwhile places, and not to Santa Monica or Beverly Hills.
Feel free to e-mail me directly if you want more specific advice for your itinerary.
Oh, and if you're going in September, know that it is notoriously HOT, especially in the Valley.