You will need to make a separate reservation regardless. They do not link resorts together on one booking, so your credits are safe. Go for it, have a great time. I think there are post's on here about organizing the transfer.
We also booked a trip and received the $500 in credits, and I just called yesterday to see if it was possible to change the dates we had booked. They said we could and that we wouldn't lose the credits, I'm not sure about booking at another resort, but you could also call and ask
I would do a new reservation for CN only and not touch your CTI booking.
Yes, they will still provide you transfer, call the 1-800 number to make the CN booking and when they ask you your incoming flight number tell them CTI. You can also have you TA make the note. When you check in at CTI, write down on your check in paper that you are transferring to CN with at depart time and everything will be setup. I would transfer early in the morning for you miss all the traffic and you may get lucking and not stop at the airport.