Ah, one of our favorite places!
When our kids were young, we didn't fly with them, so I can't help you there. I can give some WDW tips, though. One of them is one I've seen other families doing - wear the same color shirts (preferably an odd color), so it's easier to spot each other in a crowd.
First of all, go to the customer service desk when you first get there, and get them a free "first visit" button. You might not want the little one to actually wear it, because of the pin, but it will make a fun souvenir.
For very young children, Magic Kingdom has the best rides and shows. Unfortunately, MK also has the longest and slowest lines since it is one of the older parks. The newer parks have incorporated fun things to do and see, along with a bit of shade, into their waits.
There are character meets at MK, but you have to stand in a long line unless you are going in early June, and it is definately hot. Your older one will want autographs from the characters. There is a kids area in MK where the kids can go into Mickey and company's homes and do all kinds of activities. MK also has the Haunted Mansion, Pirates of the Carribean, and all of the "classic" Disney rides.
Every park has wonderful parades, but the crowds line up really, really early for them. If you want to get a great seat, find out from a cast member (what they call their employees), where the parade route is, sit down, and try not to leave your spot. Grab some ice cream or a snack before you get there so you can keep the kids occupied - for a little bit. It won't be long before they will be bored to tears. Or, don't worry about the perfect spot. You can still find a place to see the parade, though you may have to hold the kids so they can see, and the characters won't interact with them like they would if they were sitting on the curb. There are huge advantages and disadvantages either way.
At Disney's Hollywood Studios, the kids would enjoy the Muppet Show Theator. The wait for that one is indoors and in A/C, and you get to watch TV during the wait! Have your older daughter try to spot "hidden Mickeys", and look for fun things like the net full of jello (Annette Funicello... however you spell her name - the old Mouseketeer!)
Animal Kingdom has a lot of great shows (don't miss the Lion King show!), and a wonderful safari ride where you can see real animals up close. There is also a trail, like a zoo, where you can watch the animals and see gorgeous tigers in beautiful surroundings and huge bats! It is semi-shaded.
There are quite a few rides just inside of Epcot they will enjoy, and many of them are indoors, along with the line for them, and if you and your husband don't mind pushing the stroller in the heat, you can stroll around the different countries - I think the adults enjoy that part more.
Speaking of the adults, if your husband and you like to ride the rides that the kids are too young for (I highly recommend Rockin' Rollercoaster, Tower of Terror, and a couple of Epcot "big kid" rides), do a baby swap. Every single older child ride that I know of has a baby swap area. Just ask a cast member for that ride how to do that particular baby swap. You stand in line together, then when you get to the loading area, you hand the kids to one of the parents and that parent waits to the side or in a little room. When the first parent comes back, you swap the kids, and the other parent immediately rides without having to wait in line again. It's awesome!
Speaking of not waiting in line. Take advantage of Fast Passes. You can only have one at a time, but you go by the ride you want and get your four fast passes for the family, take note of the time to come back, then go ride other rides. During the appropriate time (on your fast pass), go back and ride that ride. It gives you like a 15 to 30 minute window to be there. You get to walk right past all of the other people waiting in the heat. Resist the urge to stick your tongue out...
Most importantly, especially with young children, is time management. The kids are going to be crying in the Happiest Place on Earth if you try to cram everything in. I'm hoping you plan to be there for at least 5 days, and hopefully more! Look at some literature (you can find all kinds of WDW literature in book stores, including travelling with kids), and decide what rides you want to ride, and which ones you'd rather pass on, so you'll know when you get there. Go back to your hotel in the middle of the day for a swim and nap if you have time.
Have an absolute blast! We usually go every three years, and this is the third year but we have to skip for the first time this year and it's breaking our hearts, lol!
Not sure if we are allowed to put links on here, but look up Intercot Walt Disney message board. You can find out everything there is to know there. My husband is on there daily - whether we are vacationing there that year or not! *grin*