Hi,
as per my understanding, you are trying to uplink the controller to a switch which will forward the client traffic . when you have configured different VLANs for each VAP ( Virtual AP ) you need to configure the uplink port ( Port which is connected to L3 Switch) as Trunk and you need to allow VLANs as per the requirement.
Configuration is similar to Cisco switches,
interface Fa/Gi <port id >
Switchport mode Trunk
Switchport trunk allowed vlan < list of VLANs>
switchport trunk native vlan < VLAN>
To verify use , show trunk