No problem Belle!
Let's clarify the counter service first k?
When you look at the menu, it will list Entrees and Desserts... You can pick one Entree (you'll notice that 99% of them come with fries or salad or whatever... something other than just the burger) and one Dessert -
The reason they seperate it is this: Some places offer things like a Cesear Salad, or a Turkey Salad (AK) and those don't come with fries... well, in that case you wouldn't get fries. But if you order a Sandwhich Combo - it would come with fries...
They have to clarify otherwise people will be wanting to order a Burger with a side Hot Dog... um no. Or a Salad with a side of Fries... still no.
Some entree's include things like a sandwich, beans, corn, and a drink - that would be considered a combo - so all you have to do is pick your dessert.
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Okay - now for the Sit Down Restaurants...
When you open the menu - it will list Appatizers, Entree's, and Desserts... Same goes for the ordering...
No you can't order 3 appatizers instead of an entree and dessert - No you can't order 2 desserts and one Entree...
You can order 1 Appatizer (single serving - not family sized), 1 Entree, 1 Dessert, and 1 non alcoholic single serving beverage...
The big confusion on restrictions is those few who like to make the ordering process difficult...
Some drinks are not single serving (you know, the one's that say - serves two...

- such as certain milkshakes, or souvineer cups)
Some Appatizers are not single serving (again, the one's that say - sample platters, or servings for 4 - not included)
Now, can you substitute fruit for fries? sure! Can you substitute chips for fries? Sure! Can you substitute corn for your mashed potatoes? Sure Can you substitute a Pork Chop for fries? No! don't ask!
All in all - if you stay relatively simple - the plan is simple - there are no restrictions - such as "you can't order shrimp or crab cakes as an appatizer b/c they are expensive" Or "You can't order the T-Bone b/c it's too pricey" - if the restaurant is on the list - and it is a single portion meal, you can choose what you like...
edit:
Oh there is the Captain Jack's exclusion of the "some prices may require surcharges" - Please don't expect to pay $35 for the dining plan and then walk into Captain Jack's and order the 2 Lobster Tail Dinner ($32) for your entree... that would be a surcharge. Also CJ's allows you to add a Lobster Tail to any entree for $12... don't expect that to be included in your plan either...
The plan overall is very reasonable - but it's not the "ultimate Disney scam" either... they protect themselves by limiting the expensive options...
But if you think about it - any single sit down restaurant in WDW... when adding a appatizer, entree, dessert, and drink together - you're going to be upwards of at least $40 - so this one meal would have paid for your entire day... and you still have a counter service and a snack to enjoy!
~Jess