Plan on touring at the younger child's pace. Sometimes it will be on foot, other times in the stroller. Remember, they are facinated with things we fail to notice!
You'll have a height differential for rides, so plan how you want to handle that. Who is riding first, who is swapping? What rides/attractions can each child go on? Allearsnet.com has a good list of height requirements. Also, think about what might scare either child. You don't want to spoil their fun, but you want to be prepared for their reactions.
And if mom and dad both want to go on an adult ride (ToT, RnRC, etc.), how will you handle the swap?
Tuck a change of clothes in a ZipLoc bag for the younger child--might not hurt for the older one, as well--in the stroller. Just in case! Things happen. It's amazing how many people end up having to purchase replacement clothing in the parks for one reason or another!
Be sure everyone is well hydrated and sunscreen is renewed throughout the day. Dont forget the ears and back of neck. Summer at WDW is brutal--for me, at least! *LOL* The heat is bearable, but the humidity! *eek* Better to have a lot of potty breaks than a trip to the emergency room. Been there, done that. Not at WDW, thankfully!
You may or may not want to take a break at your resort in the afternoon. Play it by ear--see how it's going. Is everyone holding up well, or has the heat and humidity taken a toll? Will time in an air conditioned attraction help, or are more drastic measures needed? Expect to take one, but be flexible if it isn't needed.
Table service meals are great, but with two young ones, you might want to limit them to one every two or three days. They can eat up a good portion of your park time. We've discovered that, even with adults, we enjoy grazing most of the time, with a serious meal every two or three days. There are a lot of food options in the park, from healthy to junk. And you can always bring in some finger foods for impromptu snacks.
Beyond that, relax and have fun. You won't be able to everything in one visit. Select the rides/attractions that will be the most fun for your family and don't worry about the rest. They'll be there in the future.