When there are multiple WLAN controllers you cannot have more than one controller as the primary. Only one WLAN controller can be the primary and another as the secondary. As far as the AP registration to the controller is concerned, it is recommended that it is ideal to set the switchport that the AP is connected to as the access port. As the client, VLAN has nothing to do with which VLAN on which the AP sits.
When the primary controller changes on the AP, the AP automatically reboots and joins that controller given that the users configured these:
You have mobility domain configured identically on both controllers.
You have mobility peers configured on each controller.
Virtual interface IP is identical on both controllers.
With mobility configured, each controller is aware which controller is out there for the AP to join as the controllers communicate this information amongst themselves, even before the AP decides to change controller. The specification of the name on the AP merely triggers that movement to a new controller.
Note: Access Point builds a table of controller name and IP address when the AP first sends out an LWAPP discovery broadcast. Hence, AP knows exactly to which controller to send the LWAPP join request.