In order to persist the Minecraft data, which you probably want to do for a real server setup, use the -v argument to map a directory of the host to /data:
docker run --name minecraft -d -v /path/on/host:/minecraft/world -p 25565:25565 timdturner/direwolf20
When attached in this way you can stop the server, edit the configuration under your attached /path/on/host and start the server again with docker start CONTAINERID to pick up the new configuration.
The following paths are exposed:
ops.jsonserver.propertieswhitelist.jsonsettings-local.shminecraft/worldminecraft/backups