How to handle different BOM types of a single product

If one has a mechanical assembly and that assembly is configured to use logical sub assemblies that define design intent and thus a logical BOM structure that we will call the Engineering BOM, how does one create a one or more variations of that BOM that may have additional levels and parts/subs and/or a removed sub level to depict the manufacturing process which we will call the Manufacturing BOM, and keep the 2 in synch throughout subsequent revisions and reconcile the differences with out a strictly manual side by side review.  I'm looking for tools for an automatic reconcile...