I don't know why the CM would tell you that you could use your credits and get a refund (you can, of course), but the better approach would be that they didn't charge you in advance, just took your CC as the guarantee. Sounds like the CM didn't explain it very well, or didn't understand it that well themself.
I'm guessing she booked online? Not having the online system properly "pick up" the associated reservation's dining plan is a pretty common thing (plus having to associate twice right now, hopefully that's part of the Oct 12-14 changes).
For the OP, there are two options to book CRT (I know, I'm sure you know this, but I'm a bit OCD about this

): Online or Over the phone.
When booking online, you have to confirm your resort reservation in the initial system to view availability beyond 180 days. If you pick CRT from this list, you will have to associate your reservations again and then search for the days and times again. Even if this is done properly, it may ask you to pay up front as it didn't "pick up" your DDP from the resort reservation. If this is the case, there are two options:
- Pay now, refund later - You can decide to pay upfront and receive a refund when you dine. This occurs quite often and usually isn't a problem at all for them to do.
- Stop and call - If you do not want to pay upfront, you can stop here (at least for CRT) and call Disney Dining to book it. They have better options for forcing it to recognize the DDP on your reservation.
There have been some reports of success in converting the prepayment to a hold ahead of time, but they are very few and far between. More commonly a CM on the phone will cancel the original reservation and attempt to rebook in the same time-slot. It's a little risky, especially if you're calling during a higher volume, as there is a chance it could be snatched up between the cancel and rebook.
The second option, calling Disney Dining, would work as well and they can typically force the system to accept the fact you have a Dining Plan associated with your reservation.