The easiest way is to have a DNS "A" record of the name Controller (ip of the wireless controller)
As they all get DHCP, one of the steps they do to find the controller is do a DNS look up of that said name. Then they will all automagically associate themselves to the controller even from different subnets and sites.
If they are off-site, be sure to set the tunnel MTU to 1300-1400 or the radios may not turn on.
The only downside to this is that you don't know what AP is what unless you have them mapped out on a floor plan via Serial number, then you can name the appropriately
Hope this helps