replies below.
Freight invoices - these are received from a supplier and then we pay the supplier but apply the freight to one or more sales orders (before we invoice the customer) so it’s really just a pass through rate but it creates a payable for us to pay and then we receive the money when the customer pays their invoice. I need freight invoice number, freight carrier (supplier), freight amount, then a child table that you select a sales order and apply an amount to. This amount then lands on the sales order in a freight invoice field.
In the sales transactions, you should add these charges in the taxes and other charges table. You can add details about fright invoice no. in the description field. Don’t go for the custom table or anything, as it should be manageable and searchable from Sales Order tax table as well.
Overall, what’s the best practice? Only #3 will have a purchase order so maybe we do our editing in the purchase order directly and just show the information in the table like I sketched and then once we have it ready, we submit to purchase invoice? Does this make the most sense? I would still have two types of invoices though?
The above work-around seems fine. It’s best to stick to vanilla and adapt work-arounds, atleast in initial phases.
Only one type of invoice, which is is Purchase Invoice. Let’s freeze it there 
You can add multiple fields in the doctype (from customize form) and set it’s visibility based on value in the other field. Following is the help on the same.