There are many ways of handling separate BOMs. It all depends on your system. One might question whether top level assembly drawings are necessary at all, particularly if you have well detailed assembly work instructions, and/or if you have product configurators that build your final product based on work orders. Many companies use BOMs on drawings, and many do not. However, if you also have a PLM, you'd be duplicating the information (having more than one single source of information), which is a faux pas in ISO compliance. In such a case, the BOM generated in CAD can be mapped to the PLM (where it would be further modified for manufacturing purposes), but not actually displayed on the Assembly Drawing itself. Or, you may just create the BOM within your PLM, using the assembly as reference only. If you don't have a PLM or ERP which maintains BOMs, then you'll likely still want to use the CAD BOM on your drawing, since that would be the only source that information would be found. I'm not even covering all the possibilities. There are many ways of handling this.