Sounds like you need to use the "Priority" and "Parent" functions.
They are laid out in the WorldGuard wiki - check it out for more information:
http://wiki.sk89q.com/wiki/WorldGuard/Regions/Introduction
The lower the priority number the further down it is on the priority 'stack'. The higher the priority number, the higher up it is on the stack. A higher numbered priority zone will override zones below it.
Take the image above for example. The Priority zone 1 is the base zone, it contains sub zones that have a higher priority. These higher priority zones will override zones underneath them.
For instance. if you have an entire section of your map zoned off as lets say, "Member-build-area" and you want to have a city with different build permissions and different members you could use the following in your configuration.
Member-build-area:
min: {z: -10231.0, y: 0.0, x: -10040.0}
flags: {greeting: Memeber Build Area, build: deny}
max: {z: -230.0, y: 127.0, x: -39.0}
priority: 1
type: cuboid
owners: {}
members: {member-builders}
bigCity:
min: {z: -380.0, y: 0.0, x: -294.0}
flags: {greeting: 'BIG CITY', build: deny}
max: {z: -281.0, y: 127.0, x: -195.0}
priority: 2
type: cuboid
owners: {}
members: {city-builders}This will allow the group "member-builders" build in the build area, but not the city and the "city-builders" to only build in the city.
For each priority area you can specify different ownership / membership. If you would like to inherit the ownership and membership of an area, simply use that areas name as the parent. In game the command for setting parent is: (taken directly from the wiki)
/region setparent TownPlot Town
And the command for setting priority is:
/region setpriority ZONE1 100
There is a lot more than I wish to cover, for this, please check out the WIKI, hoped this little spiel helped a little.
*If all else fails and your still having problems, I would be more than happy to join you in TS, Ventrilo, Skype and help you out in game. (PM ME)
http://wiki.sk89q.com/wiki/WorldGuard/Regions/Introduction
