I do that with my BV8. There is a pre defined PUC that you can select when you set up the source the the BV menu. Its called Apple Remote or Ipod remote or somethignn like this.
If that is not there, you can try just just some other device available in your list, connect the IR plug to the ATV and have it learn the commands. You just need to find one that supports the "long" button pushes that ATV expects for fast scrolling etc.
The later might be a bit smarter, because the existing Apple TV PUC that B&O provides does not send the "long" push on the go button which you need to activate the genius playlist or standby.
Cheers
JK
BS9000, BS2300, BC2, BL2500, BL3, Bl2, BS1, BV8, BC4, A8