Not to argue, but that really is not true. You can talk to several CMs and get several different answers.
I booked all our ADRs on line last weekend - including CRT, HDDR and the Backyard BBQ - it did ask me to log in my reservation # and a notation popped up stating it would utilize the dining plan. So the computer system does know when you link your ADRs to your resort reservation.
I was not charged for any of those 3 ADRs - and I printed off my confirmations, so I do know they went through.
If you are linked to your resort reservation, and it acknowledges you have the dining plan - you should see "0" balance due at check out. If you see a dollar amount due then it did not link to your dining plan and you will be charged.
This is right off the CRT reservation page -
Resort Guests & Dining Plan
If you have a Resort reservation or would like to associate your Disney Dining Plan to your dining reservations, please retrieve your resort reservation. (Please be advised that not all restaurants participate in the Disney Dining Plan. Please check your Dining Plan information for participating restaurants.) Retrieve your reservation.
Disney dining plan: You are able to use your Disney Dining Plan at time of fulfillment to pay for this reservation.
You've added the following to your cart: Grand Total Due Today: $0.00
Regardless - if you want to be safe about it, making the ADR by phone does seem to be the best option.