Your goal when organizing and packing your food and kitchen supplies should be to make things as simple as possible for meal preparation out in the wilderness.
Begin at home by preparing a detailed trip menu, complete with meal-by-meal descriptions for each day (along with basic plans for snacks, drinks and desserts). Make sure your menu includes lots of high-energy, low-bulk foods like pasta, rice, dried fruits and nuts, as well as generous supplies of fresh fruits and vegetables, good desserts and lots of quick snacks for on-the-water nibbling.
NOTE: It's a good idea to supplement any paddling menu with a few easy-to-prepare freeze-dried meals, for nights when the weather is bad or everyone is too tired to prepare a big meal.
After you've purchased your food, pack individual meals into separate, resealable bags, eliminating as much packaging as you can. Pre-mix ingredients that can be stored together (like granola and milk powder) when possible. Write down any cooking instructions that you need for each meal on a piece of paper and slip it into the meal bag (instructions printed on packages often wear off during long trips).
After packing your meals into individual bags, group the bags together so they're easier to identify (you can group all the breakfasts together, for example, or group meals by day). Finally, pack each "meal group" into its own waterproof storage bag, clearly marked so that it is easy to distinguish from the others.
NOTE: It's a good idea to pack food supplies into at least two separate waterproof bags, so that should you lose one bag in a capsize or leave it behind at a campsite, you'll still have food on board. If your paddle group includes more than one boat, spread out the food bags between boats as well, just in case your group gets separated (NOTE: this general rule also applies to fuel supplies).