I think touring with kids can be similar to touring with adults. I sometimes hear of folks who skip the adult rides if they have kids, and I think that's a mistake. On all trips, we like to try and hit every ride once. Granted, with adults only we may ride BTMRR five times in a row, and with kids, once.
Do read about rider swap. Use it, coupled with fastpasses. While the adults are on big rides, there is fun stuff for kids to do. Also, some kids will nap ina stroller. While riding Splash and BTMRR - there is a playground under the RR station. There are also sometimes characters that visit between the playground and the bathrooms. There are also two gift shops in that area. You can also use that time for bathroom breaks or for teh non-riding adult to grab some food. If you will be splitting up like that, cell phones can be a fantastic way to find each other again, and huge time saver. Of course you don't wan to use them while on rides or inshows, but to coordinate they are very useful.
Space MTn is closed, but while the adutls ride that, kids can do the TTA or Buzz (using fastpass maybe).
For Dinosaur (your kids MIGHT by big enough and able to handle it, but maybe not, it's pretty intense) you can take the kids on nearby Triceratops Spin. Kali has Maharajah trek and also an Orangatan (SP?) overhang- so you can watchthe animals while others ride. There isn't much close to EE.
For Epcot, they can look at cars while you ride TT, Mission:Space has all kinds of stuff to do inthe post show area: playground, send a electronic postacrd, penny press, gift shop, and a video game. They will be too young for the big virtual game, but eh smaller one that can play around with.
Soarin' is a little harder, since it takes SO long to get though it, even witha fastpass. I've never actaully done Soarin' standby. Your kids might be tall enough to ride actaully, but if not, then you can take them on Livin' with theLand, get a bite to eat, color (Kidcot station), or maybe do the Pumba movie (I find it very dull, and the timing would be tricky as it's kind of a long film).
In HS, try timing ToT and RnRC with Playhouse Disney and VotLM. VotLM can be slightlyintense for little kids, but there are many element so f the show they will love (bubbles). Youcan also take them thorughthe Animation Studio next door. It is good for kids, and they will enjoy the character greets at teh end. The gift shops in that area are also kind of unique. the costume one is great for kids, the art store is good for adults, and the third one is one of few places that has Little Einstein's and Playhouse Disney stuff for boys.
the kids may love Jedi training, but maybe a little young - esp inthe summer heat.
Be sure to see the Muppets at HS. Teh play area at the back of the park is also fun, but can be busy. I suggest if you have a digital camera that you do take pics of teh kids each monring in their daily outfit. It's easy and a good precaution, though WDW is amazingly safe, IMO. IF they should get seperated from you it will be good to have their exact image to show CM's.
The meal plan is a great value for kids that age. If you will be there for the start of F&W festival in Epcot, you should go, but beware that you will see adults who may be intoxicated. It is fairly rare to see public intoxication at WDw, but it is much more likely during F&W. Still, if you wish to partake, WDW is great because you can use Disney transport if you will be onsite and not have to designate a driver.
WE like to do at least one character meal per visit, but no more than two. They are fun for kids, but not quiet or relaxing. Sometimes the food is good, sometimes the non-character meals have better food. I think the food at Chef Mickeys in particular has slipped in thelast year, but maybe we hit it on a bad day. Cp also isn't as good as it once was, but breakfast there was better than dinner. 1900PF was great for dinner. The character meal at HS can be good for boys.
DO get an autograph book. It is a great learning tool for kids at that age, even if they aren't reading yet. It may be helpful to get eh more expensive autograph book where you cna put pictures in later. That way you can put a picture of the character across from the signature so the chilren can better identify each. Still many characters sign with hints: like Mary Poppins adds an umbrella to her name. You'll probably want the oversized pen they sell. A good spot to get an autograph book is your home resort's gift shop. Otherwise try th big emporium on Main ST or the WoD store in DTD. They actually sell them all over, but some kiosks only have teh smaller books. (Those will also work, but the picture ones would be better for that age group). Two other great things for kids that age are Mickey ears (find at the Chapeau on Main St. - You probably never noticed it before, it's tucked behind the Confectionary shop.) and light up toys. Kids that age just love the light up toys. You can carry it in the bottom of your stroller and take it out each night at dusk. Teh kids love them during the parade or during night touring, especially hte kind that spin. Eight dollars may seem like a lot, but if they play with it every night it will seem lke a good value. If you have a
Disney STore near you, they sometimes sell them there too (so you may be ablet o save a dollar or two).
If you'll have a car, you can also save some money by hitting the Character Warehouse in the outlet Mall just off I-4. Teh Premium outlets is theone you want. One of the other outlet malls also has a Disney store, but I think this one is better. It's also a pretty good place to go if you need any clothing items. There's even a sneaker store there (Nike and Reebok). For kids clothes, there's a Hartstrings and OshKosh. The Disney outlet sells actual Park merchandise.
With little girls, you won't want to miss IaSW. Crowds in Spetember generally aren't that bad, but I can tell you, lots of folks hit Fantasyland first thing in the am - at 9am. That is the best time for Dumbo, and you more orless always should fastpass Peter Pan. In the afternoons avoidFantasyland as it gets crazy, but at night, the place clears out! So hitting that area at night also works well. If you want to see Ariel's Grotto though, find out when she opens and get in line early. The same For Toontown. It may be best to arrive in Toontown via RR. Oh, and Donald's water boat is over there. Wet fun - so bring an exrta outfit or bathing suit or somethign.
One more tip....you may have mixed feeling abotu putting a four year old in a two piece bathing suit, but while you are at WDW, it can make life much easier. Kids that age may be so excited at WDW they don't think to go until thay are desperate: being able to get the suit off quickly can be very helpful. Also, when you enter each park, and are looking over the map - it is probaly a good idea to make anote of where the baby station/first aid is located and where most bathrooms are located. You may need to get to one ina hurry!
When the kids reach their limit - stop. Take a break. Head back to the room for a nap, or go to a quiet relaxing show. Take a boat shuttle over to a nearby deluxe resort and grab a bite to eat (the resort QS eateries and TS eateries are often more quiet mid day, plus they have AC!)) the kids may well fall asleep onthe bus ride, esp at night when it's dark. Be prepaered. I think this is when it's especially helpful to have your own stroller. I suggest a double Maclaren: lightweight, easy to fold, has baskets to carry stuff.
Do bring an extra outfit aroudn each day. DO bring a rain cover for the stroller. (and the kids!) You will almost certainly need it that time of year! Short, and not so short downpours are common that time of year. But don't despair- every day will have a "chance of thunderstrom' in the weather report. That doesn't mean it will rain all day.
If you have skipped shows in the past, consider seeing more of them. They are an entertaining way to give your kids some semi-downtime, often to cool off in AC, and many are truly excellent! FotLK is a favorite. B&Beast at HS is also well done. WE're not big on parades, but kids that age may well love them. Spectro at MK is fun - though you may not have many chances to see it in September when there will be many halloween parties going on.