I am having this same issue- I would like my sales receipts to say- Paid in Full in the note section, but obviously do not want my invoices to say that !!  But when I make a "new template" for sales receipt it changes the section in all my invoices as well ?!?! Craziness.

I am assuming they never got back to you with an actual answer though.

Thinking I will have to have a Word document with the phrase I want and just copy and paste each time. 

Just nuts when they bill this as being able to make custom templates !