There's two levels to this. The cluster autoscaler instance location and then the kubernetes pod location.

Create an auto scaling group for each availability zone:

• Cluster autoscaler does not support Auto Scaling Groups which span multiple Availability Zones; instead you should use an Auto Scaling Group for each Availability Zone and enable the --balance-similar-node-groups feature. If you do use a single Auto Scaling Group that spans multiple Availability Zones you will find that AWS unexpectedly terminates nodes without them being drained because of the rebalancing feature.

Then for kubernetes, use pod anti-affinity on the EKS populated failure-domain.beta.kubernetes.io/zone label.

EBS Volumes don't span availability zones so if you are using persistent volumes you may get stuck with pods in one zone or worst case pods that won't schedule.