It depends on what you booked.
If you just booked a room (no package, i.e. no tickets, dining plan, etc.) then you can call Disney (you HAVE to do this on the phone, I don't think the website allows for this). Give the CM your reservation number and find out whether your dates and room are eligible for the CAA discount (tell them it is the Canadian version of
AAA if they don't understand what you are talking about). If there is availability, they will ask for your membership number and adjust your rate.
IF, however, you have booked a package, you MUST go through the CAA
travel agency. Disney cannot apply the CAA discount to a package. You will need to cancel your Disney reservation with them, and contact your CAA travel agency. What they do is book your package and apply the discount to the room portion only. You will pay regular rates for the dining plan and/or tickets. If a public code comes out that you are eligible for, CAA can contact Disney and have it applied, but then you will lose the CAA discount on the room portion of the package - as per Disney rules, no "stacking" discounts. Make sure before you do this that the code saves you more money - although it usually does.
I hope this helps.
One other alternative to be aware of is that if you are NOT getting the dining plan, you can book your room-only reservation with either CAA or Disney and go to CAA to get the park tickets. They sell them at a slight discount to CAA members, so you could save a little bit more. IF, however, a code came up that required a package vacation, make sure that you could return the tickets to CAA and then have them change your reservation into the code discounted package.
Yes, this is all very confusing at times. My wife often thinks I'm nuts for keeping on top of this as much as I do... but we basically won't go unless we're saving somewhere between $600-$800 on a Disney vacation which would cost around $3,600 at full price. I'm totally willing to do the leg work and research to save that much - and we have. Although for our hopeful trip this summer, I still haven't found an offer which will do that - but there's still time!