Optionally, you can define SSID groups. An SSID group has SSIDs as members and can be specified just like an SSID in a FortiAP Profile.
Go to WiFi & Switch Controller > SSID and select Create New > SSID Group. Give the group a Name and choose Members (SSIDs, but not SSID groups).
config wireless-controller vap-group
set vaps "ssid1" "ssid2"