peeing in the food dish is pretty common.......i would give her lots of hay. Alfalfa hay, grass hay, any and all hay. Most people who litterbox train bunnies will often throw a bunch of hay into the litterbox and bunnies like to sit in there and eat it. Yes they will pee on it but not all of it. I would do that. I would let her pee in the food dish and then dump it into the corner of the litterbox so she gets the idea to pee there instead. She should pick a corner of the cage and use it. Might take some time though. Once she figures out to go in the litterbox, she should not go in the dish also. But if you have the dish in a certain area of the cage, put the litterbox there instead.....and put the dish elsewhere. Rabbits are pretty particular about wanting to go RIGHT THERE, wherever it may be. Once they are used to go in the litterbox, you can often move the box and they will follow it.....but in the beginning, go with the flow.
I would also put a bunch of hay CUBES in there. Loose cubes. Not in a dish or anything. She should chew on those if she is hungry and her food pellets are peed on.....