You could do both, but it would be very time consuming. If you're ok with that, go for it. I think the timing would be fine, unless you're a larger party. I'll also warn that 50s Prime Time has some good desserts and shakes, possibly better than the shakes and offerings at Sci Fi.
We love both restaurants and think they are the best themed on property. For dinner, I tend to lean towards 50s Prime Time because the entrees are heartier - fried chicken, meatloaf, etc. Its a heavier meal and the portions are larger, so keep that in mind when considering dessert elsewhere. The fare at Sci Fi can be lighter and more lunch-style to us. They both are super unique atmospheres to dine in, but I think the theme of 50s Prime Time is often lost on the younger kids. The car-style table at Sci Fi is usually a hit with kids. I don't think you can go wrong with either. I wouldn't do both personally. I would decide based on what my plans are for the rest of the day (dining, park, rides, FPs, etc) and which time works better with our schedule.