Thanks for writing, Peter!
It is basically the exact same to make an Advanced Dining Reservation with or without the dining plan.
To make reservations, you can either call by phone (407-WDW-DINE / 407 -939-3463 ) or you can do it via the internet at
http://disneyworld.disney.go.com/reservations/dining/
If you call by phone, the operator will sometimes ask if you will be using the dining plan, but this is mostly just for their planning purposes. In my experience, there is really no difference if you mention that you are going to use the dining plan for your meal or not. If you already have the dining plan, by all means, let them know. If you add the dining plan later, feel free to call back to update your reservation, but I personally don't think this is absolutely necessary.
The most important difference with having the dining plan is that
once you are at the restaurant, you should tell the host and your server as soon as possible that you will be using the dining plan, so they bill you correctly.
I should also mention that it is a very smart idea to
make your dining reservations BEFORE you get the dining plan. If you can't get the dining reservations that you want (or suitable substitutes), then you probably should reconsider getting the dining plan.
Hope that helps.