In reality, I have rarely run out of battery on even a long run, but I tend to take the case anyway - call me paranoid.
You can run with one in and one charging in the case though and then swap them over if needed, though it's a bit fiddly to do while running. Airpod Battery lifeīattery life is good for AirPods - it can be 5-6 hours, and then you can charge them all over again in the case 5 times, but lifetime is impacted if you have the volume up high (>90%) to cover the sound of traffic for example, where It can drop to 2-3 hours. This has the added benefit of having a keyring loop so I can attach a Tile to the case as well - in fact, I permanently keep the silicon case and Tile attached to the AirPods now - save's me running around the house in a panic trying to find them every other day. I sometimes take the charging case with me on a long run too - and so I got a nice waterproof one from Amazon. I now give them a little wipe before putting them back in the case after a run, and it seems to have fixed it. I initially thought this was a hardware issue and Apple support did too, happily sending me a new AirPod and a new case, but I had similar issues with the new stuff. So I have pulled them out just before a run, only to find one of them is not charged. I have had some issues with AirPods seemingly getting sweaty and then not charging in the case.