I have a production process I have to solve. My company needs to create an additional Purchase Order for a Raw Material associated with the items ordered before the finished good items on the SO are assembled. What is the best way to create a standalone PO and when saved, links in some way to the original sales order? Also, Can the SO have a link somewhere to the additional PO?

You can add a custom field to the PO or SO (or both) that is a list/record field. Where the record type is transaction. Then assign the SO or PO in that field