Option and notes fields after cart at checkout for order, not just line items
First, add a custom field to your orders, let's call it orderNotes.

Then, in any updateCart form, you can use an input with name="fields[orderNotes]" to set the value of that field.

(Line items persist on the cart until the end of checkout.  At that point they become a saved snapshot of those line items on the completed order.)

&lt;form method="POST" &gt;
       {{ getCsrfInput() }}
       &lt;input type="hidden" name="action" value="commerce/cart/updateCart"&gt;
       &lt;input type="text" name="fields[orderNotes]"&gt;
       ...etc