Hi,
Yes you can start using all APs along with IAP with a Controllers, bring up a setup by terminating APs on the controller .
you have two solutions for IAP,
1. Configure the SSIDs with the similar security in IAP but enable L2 centralised tunnel with the Controller for centralised management
2. Simply convert your IAP to AP and terminate on the same controller.
Please feel free for any further help on this.