Here's what you'd need to do to 
1) control OS X (or any other app with Apple Remote support) when XBMC is not running 
2) launch XBMC with the menu button 
3) control XBMC when XBMC is the front application 
4) not use Remote Buddy's menu at all

Just follow these steps: 
1) In Prefs > Behaviours: untick all checkboxes in the list view on the left except for the one in front of XBMC 
2) In Prefs > Mapping > Global Mapping: remove all pre-mapped actions (by setting them to "-") 
3) In Prefs > Mapping > Default Behaviour: 
a) Select "Behaviours > Activate XBMC Behaviour" for the Menu button 
b) Select the respective "Virtual Remote" actions for all other buttons (i.e. "Virtual Remote > Left" for the button "Left").

Best regards, 
Felix Schwarz