I EDC a P2D and P3D. In a belt pouch that holds other things as well, I carry 3 spare primary CR123s. I have had my battery die while I was using a flashlight, so an extra flashlight, and extra batteries, do come in handy. If I'm carrying a bag, I have 3 more spare CR123s (and I'll carry more if I'll be gone for a long time).
I carry spare batteries by wrapping them in saran wrap and then clear packing tape. It's simple, cheap, quick. Easy to open with a knife. There's no empty container to carry around once I've used them. The more water resistance you need, use more saran wrap. The more wear resistance you need, use more tape. Can work with any number or type of batteries. Depending on the shape of the pocket/bag you're carrying them in, can wrap them side by side or end to end. And you don't end up carrying a container that's significantly larger than the batteries it contains. Obviously not a good idea if you're scuba diving, but should hold up well enough in your pocket if you get rained on.