You have to configure QoS on WLC and then it will push it to APs (even traffic does not hit WLC, AP level it inspect upstream & downstream direction and apply QoS).
Refer to the below design guide for more details
https://www.cisco.com/c/en/us/td/docs/wireless/controller/8-5/Enterprise-Mobility-8-5-Design-Guide/Enterprise_Mobility_8-5_Deployment_Guide/ch7_HREA.html
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For WLANs that are centrally-switched, the FlexConnect AP handles QoS in the same way as standard APs. Locally-switched WLANs implement QoS differently.
For locally-switched WLANs with Wi-Fi MultiMedia (WMM) traffic, the AP marks the dot1p value within the dot1q VLAN tag for upstream traffic. This happens only for tagged VLANs, not the native VLAN.
For downstream traffic, FlexConnect uses the incoming dot1p tag from the locally-switched Ethernet and uses this to queue and mark the WMM values associated with frames destined to a given user across the RF link.
The WLAN QoS profile is applied both for upstream and downstream packets. For downstream, if an 802.1p value that is higher than the default WLAN value is received, the default WLAN value is used. For upstream, if the client sends a WMM value that is higher than the default WLAN value, the default WLAN value is used. For non-WMM traffic, there is no CoS marking on the client frames from the AP.
Cisco strongly recommends that appropriate queuing/policing mechanisms be implemented across the WAN to ensure proper handling of traffic based on its DSCP setting. An appropriate priority queue should be reserved for CAPWAP control traffic to ensure that a FlexConnect AP does not inadvertently cycle between connected and standalone modes because of congestion.
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At the switch level, you have to trust QoS settings made by AP in order to preserve it.
HTH
Rasika
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