Hi Steve81,
Thanks your sharing your business scenario. There is no OOB feature in the system to create SO invoice by line and enable to create payment against specific SO line. This requires customization.
However, There is a work around solution to meet your requirement but that can only work when you know an exact amount client will pay for 1st Invoice and 2nd invoice
1. Create a sales order with 02 lines
2. Goto header section > Currency Tab > Select Payment Schedule and save the changes
3. Go to Invoice ribbon > Bill >> Payment Schedule
4. Break down the invoice amount as agreed with customer.
5. Post the invoice.
6. Create payment and you can select respective invoice, client is paying you for.