Make time for nap time. I go to Disneyland once a month and what I see are kids that are your kids age cranky and fussy bc they are tired, hot and been walking all day. Since you have a 3 yr old and 9 month old they won't be able to do much so one of you will have to stay behind while the others do rides so prepare for that. Bring something for them to do in line. Sometimes lines are up to 2 hours. I'm 35 and I get so bored, I can't imagine a child in line. Map out your route. Research the park so you don't have to go to one area to the other and them back to the first. Figure out the top rides you want to do in each area so you can do those first and get those out of the way. Have fun and good luck with the kids!
To make the trip go smoothly, only carry the things that you need and make use of rental lockers instead of carrying things around. In addition, it is also advisable to measure your kid's height and take a break during the busiest time of the day. For more tips visit http://gocalifornia.about.com/cs/disneyland/a/gentips.htm.