I use a duffel bag, which obviously isn't waterproof. However, there are plenty of fishing tray options out there that could help you organize things. The duffel I have has an outer pocket on either end, 2 on the sides, and a main bag/pouch.

Many, many options out there. I suggest you peruse Galls.com, North American Rescue, Dyna-Med ... Depending on the size of your kit and budget, you can usually find a great bag or hard case to help organize. At the very least, see what you don't like and find features you do.