Tips are always based on what you eat - you as the patron have the discretion to tip for good service, but you tip based on what you ate. It's not the server's issue that Disney has supplied a discounted meal plan. If your bill shows that you ate $100.00 worth of food at one meal (before taxes), then you tip based on that amount, as that is what goes to the server for his/her hard work in serving you. The server should never be penalized for Disney's meal plan.
We are doing the Deluxe Plan as well, and so for example, our meal at California Grill will be more than what we paid for the entire day ($69.95/person) of the meal plan, but we have to tip based on whatever food/drinks we consume, not based on what we paid for the plan.
Hope this helps, Tiger