Hi,
My DS is almost 3 and we have had annual passes since before he was a twinkle in our eyes and continued to go to DL and CA after he was born - he has probably been to DLR at least 50 times!!!
Here is my 2 cents worth:
1. Make sure you have a stroller for both! Your 3 year old will need one - mine naps in ours for an hour or two usually (that's when I go shopping on Main Street LOL).
2. Ask the CM's about the "Baby Swap Rider Switch Passes" at the line entrances for all height restricted rides.
3. If you bring in juice or water into the park with you (for sippy cups) they will give you a cup with ice for free at all the food areas to add to it to cool it down during the day.
3. Fantasyland and Toontown both have tons of stuff for your 2 kids
4. If you go to Ca Adventure check out the Redwood Creek Challenge trail - your 3 yr old WILL LOVE IT!
5. Our favorite character meal is breakfast at the Plaza Inn on Main Street with Pooh & Friends (kids under 3 eat for free).
6. Use the Carnation Baby Care Center! It is on the end of Main Street and a great (quiet) place to change diapers and feed babies that need to get away from all of the over stimulation and heat!
7. Take sunscreen and water with you.
8. My ds loves the parade at DL but is FREAKED out by the Electrical Parade (which I never expected) You never know what will spook them so just go with the flow and let them set the pace!
9. Small World is the all time best kids ride in the universe
10. TAKE LOTS OF PICTURES!

Good luck you will all have some great memories!
HAVE FUN!!!!!