SIP/H.323 is common VoIP protocol and based on TCP/UDP for management, RTP for data stream.
So either you have an host controller with SIP/H.323 stack running and use FXT009 as modem; or you can implement these protocol using WIP library and use FXT009(or other OpenAT device) in standalone mode.
Please refer to the spec of both protocols, e.g. SIP - RFC 3261, for details.
Still, if you are planning to implement and run SIP/H.323 stack inside FXT009 OpenAT for voice call, you may consider the audio interface as which the built-in analog audio may not support the SIP/H.323 audio stream.
Hope it helps and let us know the progress of your development.