HI James-
Actually there is a bit more to set up. We are just about to release the config guide for the Lync SDN API. I will DM you with the pre-release version.
In short you need to configure the lync web listener port in the web-server section. If you are going to use https you need to make sure you have trusted certs on the lync and aruba controller. For http you can use IP for https you MUST use an FQDN. The guide goes through that as well.
Then you need to modify the LyncDialogListener.exe.config file after the install to send the controller the right values.
Finally you need to ensure that classify media is turned off on the ACL used to detect Lync traffic.
John