The note was included at checkout so you won't see a copy of it in your eBay messages. This is a standard note included by people using you as a drop shipper and people sending gifts. As long as you upload tracking to the transaction, eBay will send that info to the buyer. There's no need to send them a separate message.
If you want to duplicate efforts, though- you can either use the contact buyer link on the transaction or the contact member link on the buyer's feedback page. Either will work for sending a message. Neither route will include the note the buyer left at checkout. I hope that makes sense.
