In my case, due to the Hub placement, I found out that the BL5 IR eyes are not easy to activate, so I have defined my system to send the IR commands from the Harmony hand piece.
Don't forget that you can send IR commands from the hub using the two IR extenders as well...
Currently in my setup the Harmony is only used to control the non-Beo AV gear. All mounted in a cabinet, so is the hub, so it blasts IR inside the cabinet to everything, except the TV which is wall mounted. I use one of their IR blasters sitting below the TV and pointing out from the TV but it still operates the TV perfectly. Next up will be adding my BS9000 to the mix, eventually (meaning when I get the remote, a cable, and my laptop in the same place). Not a high priority to me.