There's an old adage in Hollywood warning directors never to work with animals or children. Roger Rabbit not only does both, but its animals and children are animated, and not in the hopped-up-on-too-much-sugar sense. This film isn't the first one to blend live action and animation, but it is the first to do it so convincingly.
To make it look as if Jessica really was teasing Marvin Acme at the Ink and Paint Club, or Valiant really was hiding Roger in the sink, Zemeckis filmed his scenes just as he would if Roger and the gang were real life actors. It was up to editor Arthur Schmidt to make the final product look as genuine as possible, and he won the Academy Award for Best Film Editing for his efforts.
Many previous films that blended live action and animation filmed their scenes with a static camera. Zemeckis didn't understand why he couldn't pan and zoom the camera like normal. When he asked animation director Richard Williams why older films were made with so many static frames, Williams chalked it up to laziness. "The problem is going to be time and money," he said. (Source)
It was twice as much work—and about four times the money allotted for the original budget—but they did it, and they got two more Oscars for their efforts: Best Sound Effects Editing and Best Visual Effects. Williams also won a special achievement award for his impressive direction that flawlessly combined animation and real life. Only sixteen of these special awards have been given in Oscar history.
The film was a financial success too, not as if that part really matters. But hey: they can afford to take risks. Disney isn't exactly scrounging for pennies in the couch cushions.