You can make the res online. Besides being signed in, you need to click on the blue link at the bottom of the res page that says something to the effect of "I want to use a dining plan for prepaid reservations." Also, the dining plan can only be used for certain seating categories/dinner show times so be sure you're choosing correctly.
If you go ahead and pay in full, then decide to call the dining line, be VERY clear to the CM that you want to keep the res, but only want to change the form of payment. Otherwise the CM may choose the easiest method of refunding the payment which is to cancel the current res, then re-book. However, there's no guarantee that between the time of cancelling and re-booking someone else won't get the res.