Wrestling with similar issues.  We configure products to order at the time of shipment.  Have the sales end of the process down and working 'ok' but trying to figure out how to implement 'production work orders' for our prekitted sub-assemblies. This is so that the team can figure out what kind of time is required, what inventory parts are required and put a schedule together.  As far as i can tell, our QB Enteprise Platinum with advance inventory for manufacturing doesn't understand the concept.  So I'm headed down the path to create a Production Work Order template from a purchase order template, and create 'service' items that can be applied to COGS, then offline mash stuff together in spreadsheets.   Or...just something like Fishbowl or another ERP/MRP that is reasonably priced.