There is not correct way to manage more than 3 zones on endian.
It's a pity, but you must group the VLAN's on these 3 zones, and if you need DHCP server on endian you must manually tweak the dhcp.conf.tmpl template.
Also check
http://help.endian.com/entries/25391848-How-to-split-a-zone-in-sub-zonesfor correctly separating traffic between VLAN's. If you don't do that you can have a nice packet storm (I made only by connecting 2 endians on the same VLAN's).