When I deploy for local and remote sites, I create an "A" record of Controller with the IP of the Wireless Controller. You also have the option of a DHCP option 43.
This will point your AP's to the controller no matter what vlan/subnet they are on as long as they can resolve the name. Also, when deploying to a remote site, it is good to start your MTU Size at 1400. Anything higher than that, the AP may associate but the radios will not turn on due to packet fragmentation.
Please let us know if this does not work for you and if there is anything else we can assist you with 🙂