1. Filesystem layout
On both deleuze and mire, BIND data lives in /etc/bind. This directory is seeded with the default files from the Debian bind9 package. Additionally, we add a zones subdirectory.
DomTool periodically deposits /etc/bind/named.conf.local, listing all of our hosted DNS zones and their master/slave statuses and configuration. DomTool also populates /etc/bind/zones with zonefiles referenced by /etc/bind/named.conf.local.
1.1. Permissions
/etc/bind/zones should be owned by user bind, since BIND seems to like creating temporary files there. I've only yet seen this matter during updating of slave zone information.
2. Adding new HCoop subdomains
This is not done by editing anything in /etc/bind. Instead, see DaemonAdmin/Tinydns.