There is an option on the NOTES screen in the ticket, to select DO NOT PRINT so the note won't show up on the ticket.
PAID (PD) notes have priorty over the ESTIMATE (EST) and OPEN (OPN) notes.
When printing 2 Copies of the invoice, it will indeed print two copies but only one copy of a new page note. This happens, being most times the second copy is for the shop's record and therefore they don't need a copy of the note.
When status is set as ESTIMATE it will show both the ESTIMATE and the OPEN notes.