converting sales orders to invoice

converting sales orders to invoice

I run a business buying and reselling parts

-we send a quote
- my customer sends a PO
- we raise a sales order and send them a confirmation (I put their PO number in the reference field)
- we send the invoice when I ship the product

what I see is that when I convert from a sales order to an invoice 
a) the customer PO number does not get put on the invoice- and also
b) on the invoice there is a reference for PO number, but this number is actually my sales order number

am I missing something here- I need to be able to put the customer PO number (in the sales order reference field) on the invoice so that I can get paid. I have tried modifying the template but it does not offer this