Hey - I have a six year old and two year old twins too! :woohoo
We were there in December, and all in all, it was a great trip. My girls (the twinnies) did very, very well. We stayed at SSR, so I can't help with the hotel bit, but I can tell you what helped us in the parks.
They are not big stroller babies, but I really lucked out. We made sure to let them run around for a while and then we'd throw them back into the stroller for drinks and snacks. My girls will not wear a harness - we've tried several times and they morph into demon children and apparently believe that any type of harness or restraint is a punishment. There was just so much for them to look at, I really never had much of a problem getting them to stay in their stroller, and the few times they fussed about it I either gave them a lollypop (I bought those little dum dum pops with us from home) or I would blow bubbles.
My girls had a hard time with the buses at first, I don't know if it was the noise or not being in the car seat, but they did NOT like them the first few times they rode. After that, they were fine. However, the WAIT for the bus was something that was hard to deal with. Again, we would let them walk around with one of the adults while another adult would wait in line for the bus.
In the Magic Kingdom:
My six year old is a HUGE Buzz Lightyear fan, so he enjoyed Tommorowland and Buzz Lightyear's Space Ranger Spin quite a bit - he would've ridden it all day. My twins also liked that ride, amazingly enough. My DS also liked the Tommorowland Transit Authority, he thought it was neat to go above Space Mountain and Buzz Lightyear.
My twins LOVED Pooh's Playful Spot (so did my son!). This is right by the Pooh Honey Pot ride. It's a cushioned play area with a slide and things to climb on, they all had a blast.
Mickey's Toontown Fair was also a big hit with all three of them.
In Epcot:
My six year old liked looking at all of the different countries, and REALLY liked the Innoventions "play" area. There are just a ton of different things you can do there.
My girls favourite thing here was the dancing fountains and Figment.
All three liked the Living Seas, we spent a loooonnnnngggg time in there. Also, the food pavilion was great! Some of the best food we had and something for everyone in one place!
In Animal Kingdom:
All three - anything with animals. We rode the Safari twice and went on every single one of the walking trails. The boneyard was wonderful, I practically had to punish my son to get him to leave.
In MGM -
My kids liked the shows, especially the Playhouse Disney, Voyage of the Little Mermaid, and Beauty and the Beast. Even my son liked the shows, and he's usually not into any of those characters.
Have a great time - let me know if there is anything else I can help you with!
Counting down to our next trip in May!!! 
Whenever you are in the parks and you buy something and do not want to hold onto it, you can have them send it to your room and the hotel. This is free of charge and usually done within 1 to 2 days.
