Beo6 will use IR just like the Beo5 for all current Beovisions and Beosounds.
In addition it will connect using WIFI to the Beomaster 5 (if they release a software update) and Beosound 5 encore to display the album art and navigate through the music library on the remote itself.
In addition, I am guessing (and hoping) that if you have a MLGW, the Beo6 could connect to it to control the home automation system.
Currently, you can send some commands to the home automation system, but you cannot get feedback and status.