I'm sorry I can't quite follow you. Do you mean you have created two AP Groups, and you wish to apply the different WLAN Group to each?
From Configure/WLANs, have you setup two WLAN groups, each with the SSIDs you want?
Then from Configure/Access Points, under AP Groups, define a new group (not System Default), and under Radio Settings, there is a WLAN Group option to "override System Default", which is a dropdown, and should show the alternate WLAN Group you defined.
If you made two different WLAN Groups, you should be able to assign them to the APs in two different AP groups, with this override setting. Make the setting on both radios if you have dual-band radios. I hope this is helpful.