Design/Engineering BOM to Manufacturing BOM

Parts and assemblies built in CAD may be structured in a way that suits design (references, master parts, logical grouping etc). However, this structure does not always reflect how it gets built physically. Have an effective way to customise BOM to reflect: 1)As designed; 2) As manufactured. Currently I'm thinking this would be done by manually building a BOM in Duro browser, then connecting CAD (ie. the reverse to typical CAD CPN Pull). But it would be good to develop a more streamlined method.