With the exception of a buffet or Victoria and Albert's, it seems that waitstaff in all WDW restaurants are very used to having people order any and all combinations of food ---- appetizers as entrees, splitting entrees, desert only, etc. If you have any doubts, call the restaurant once you get there and ask.
Also, if there's food you "sort of" like, but not with the fancy sauce or mushrooms on it, or not the veggies/starch accompanying it, just ask if it can be prepared plain or slightly different. Also ask if different veggies/starch can be substituted. We haven't had special requests very often, but there was usually no problem (unless the meat was already marinating in something like terriyaki sauce --- then call ahead to ask if you can get some plain meat) .
Hope you have a great trip!