Personally, I use blue masking/painters tape to tape off individual areas..... for example if buff a handle, I'll carefully tape the guard and/or buttcap, then CAREFULLY buss the handle.  Then I'll tape off the handle I just buffed, and do the rest of the knife in that manner.   It's helpful to put a coat of was on areas you just buffed before taping.....  makes the tape easier to remove.  
  Another thing I do is choose the materials I use carefully..... I try to stay away from blonde (light colored) handle materials that would pick up polishing compounds.     The longer I make knives, it seems the less and less I use a buffer, and the more I depend on fine hand finishing.