How many days are you going for? You will find a lot of useful info on the Disneyland board, but I've been to Disneyland over 10 times (I think?? lost track somewhere) and I'll try to answer a few questions.
Firstly, I wouldn't bother with Universal. It has very little to interest kids the ages of yours. If you are renting a car (we usually do ) think about going down to
Legoland in Carlsbad outside San Diego. I think it's about a 1.5 hour drive. Your kids are just the right age. My son was 5 when we took him there and he loved it. It's really cool for adults to see also.
I wouldn't bother staying on property in Disneyland unless you can get a great rate. Generally the hotels are much more expensive than WDW and there are many non-disney properties which are actually closer. Only the Grand Californian is really close enough (has it's own entrance actually) to be worthwhile and it's very pricey. The Candy Cane Inn is walking distance and also has its own bus if you can't do the walk. (most other properties use the ART system which is not free and is shared) It is a motel style as most walkable ones are but is very nice. My personal preference lately has been to stay about a mile down on Harbor Blvd. There is a nice Embassy Suites (more room for your family), a very nice Hampton Inn , Hilton Garden Inn, etc. I prefer these as they are proper hotels with interior corridors. The ART (Anaheim Resort Transit) services these, but I don't kow the cost. As I said we usually rent a car. If you buy your parkhoppers at CAA (you don't have to be a member) you get free parking at Disney. Otherwise it's about $10 per day with in-out priviledges. Check Tripadvisor for hotel ratings under Anaheim and Garden Grove to get other ideas for hotels.
As far as dining goes, its not the big deal in Disneyland that it is in WDW. You might want to do a character breakfast though. We also enjoy Storytellers Cafe in the Grand Californian for dinner.
September is a good time to go for fewer crowds. If you haven't already, you should buy the Unofficial Guide for Disneyland. It has a lot helpful tips especially for travelling with little ones.
Most of all, as others have said, it won't be perfect, but it will be fun. Try and go at your kids pace, give them lots of down time and realize that you will probably go again someday and you don't have to do it all this trip.
Good Luck!