Not sure I really follow everything there.
For starters, you should have this table structure:
You place a portal to LineItems on the orders layout and define fields in LineItems that look up values--such as a price from products.
LineItems records should be linked to a single order, it should never be the case that a given line item record is on more than one order record. You would, in many cases, have different line items for the same product on different orders, however and I think this is where things are getting confused for you.
Here's a simple invoices Demo file created by Comment that illustrates the above set up:
I think you are correct. This is where I am confused. The proverbial Light bulb is shining bright. Thank you. I should have asked this question 10 hours ago.