Search for "Bill of Materials Multiple Configurations" in the SW help.
Alternatively, check out: http://gupta9665.wordpress.com/2010/12/17/multi-configuration-in-assy-bom/
Hope this helps.
Ah the challenge. Getting people in the aerospace/military world to accept the fact that SolidWorks and other automated 3D CAD systems do not support the "matrices parts list."